Secret Bases:

Throughout the Gen III Hoenn games you would sometimes see different looking trees, indents in rocks, or odd shrubs. If you had a Pokemon with the move Secret Power, you can use it on these trees, indents, and shrubs to create a Secret Base. You could consider Secret Bases as your "home", you could decorate it with furniture, ornaments, plants, posters, and of course, Pokemon Dolls. However the main point of having a Secret Base was when you Mixed Records. Mixing Records was a feature that let players swap around certain information, one being where their Secret Base is and how it looked. Not only that, a trainer representing that player will be in their Secret Base and can be battled with the Pokemon they had on them when you mixed records with them.
Of course all that was back in the days of needing a Link Cable to trade and battle. Now that we have WiFi, a whole slew of new possibilities arise. Maybe using a version of XY's PSS, we can tap on a random player and visit their secret base if they made one! That would add in a whole new way to interact with other other, especially if they expand the number of decorations to make trading of decorations another challenge. Or maybe let us turn our Secret Base into a sort of Gym-like place, allowing us to build essentially our own gym with a puzzle to solve, maybe trainers to battle (bonus points if said trainers are other players they have registered as friends), and finally them acting as the "Gym Leader". And to make a point of all this, its recorded how many Secret Bases you've defeated and give you a rank based on that. Said rank can then be seen by other players when they enter YOUR secret base, so in a way its used to show how "challenging" you are. Of course the above scenario I mentioned have many problems to it, but I'm just brainstorming and pointing out one of the possibilities you could now do with Secret Bases.

Diving Underwater:

In Gen III a new HM was introduced, HM08 Dive. While surfing over dark patches of water, you can use Dive to go to an Underwater are which matches the Route you're in. Diving was mainly needed to access important areas in late game like the Seafloor Cavern and Sootopolis City (and the Sealed Chamber if you wanted to catch the Legendary Golems), though other then that there wasn't really other reasons to dive underwater except to find items or catch some of the Pokemon you can find in the seaweed.
Now that we've moved to 3D they could possibly now do more with the underwater. For one they no longer need to be restrained to one plane like with the Gen III (and V) games. Of course while this means we may have to deal with swimming controls (which throughout the history of video games haven't had a kind relationship with one another), this does mean they can create a big area for us to explore and to hide things in (maybe even introduce underwater Secret Bases). And with a bigger area to do things in also means the more they can expand upon the diving mechanic and make is more then something which mainly only purpose was story progression and extra puzzle step to getting Legendary Pokemon. For example, how about being able to find trainers while diving and having Underwater Battles, battles that you can only use Water-type Pokemon or Pokemon in the Egg Groups Water 1, Water 2, or Water 3 (pretty much a copy of Sky Battles). Or how about have Water-type Pokemon swimming around and if you make contact with it we'll enter a battle with it (and if its a school of Pokemon it'll be a Horde Battle). How about a side quest where people tell us about items they've lost while crossing the seas and we can go and retrieve those items? There's a lot they can do, of course the question is will they? Though if they do anything, I hope they make underwater look beautiful like they did in the Marine Tube.

e-Reader:

The e-Reader was a Gameboy Advance peripheral that allowed you to scan cards with special bar codes on the side which could do various things. Some games were even compatible with the e-Reader, including the Gen III Hoenn games. Sadly the e-Reader, though popular in Japan, wasn't in the United States so its connectivity to Emerald and the Gen III Kanto Remakes were removed from international versions of the game. However Ruby & Sapphire still had their connectivity to the e-Reader and some cards for it were released outside of Japan.
So what were these cards? Well there two finds, first was the Pokemon Battle e cards that was programmed with a special trainer you can battle in Mossdeep City and sometimes the Battle Tower (they may also have Pokemon not in the Hoenn National Dex or even a Legendary). Second were cards that gave you a Berry not found in the game (nor any other game afterwards)! They were mainly PokeBlock ingredients with some having effects but nothing that another Berry already had (however the Eggant Berry did have the unique effect of curing Infatuation).
Why do I bring this up? Well the 3DS can scan QR codes so maybe they can release QR codes which does the same thing as the e-Reader cards once did. They couldn't need to release cards either, they can just put a QR code up onto the main Pokemon site which lets you download a special trainer or berry. They could even add more trainers (though no Berries, but it would be interesting for them to reintroduce the e-Reader Berries permanently)!

And I think that's all the features of Gen III I wanted to talk about. Next are mechanics and features from future generations which I think we should keep in mind:

Generation IV Features:

Pokemon:
Gen IV was the last Generation to released new evolutions and per-evolutions for past generation Pokemon (sans Gen VI which ONLY introduced one new evolution, Sylveon for the Eevee family). Some of these Pokemon were ones introduced in Gen III: Gallade, Probopass, Budew, Roserade, Dusknoir, Chingling, and Froslass.

Now in FireRed and LeafGreen they actually prevented non-Gen I Pokemon from appearing until post game, however in HeartGold and SoulSilver they must have decided that didn't make sense so if a Gen I or Gen II Pokemon got a new evolution in Gen III or Gen IV you were able to get that Pokemon. I think they'll follow HeartGold and SoulSilver's example by just adding the above Pokemon to the Hoenn Dex.
However there's another reason why I mentioned these Pokemon an that's their relation to some important characters:

Wally: Wally if one of your "rivals" and the player's father helps him capture his first Pokemon: a Ralts. Well, "rival" may be an exaggeration, you only battle him twice (once after he captures his Ralts and the final time right before the Pokemon League (mainly because your actual rival, the playable character you didn't pick, decided to focus on their studies thus was no longer battling you)). In the game, no matter what Ralts he caught, it would always be a Male Ralts and in his final battle he would have evolved it into a Gardevoir the final time you battle him. Now I think they should make Wally a bit more involved in Omega Ruby & Alpha Sapphire, he has an interesting story and the other playable character was never really your rival. It would nice for Wally to act as a normal rival and battling you time to time. And to further emphasize this they could also give him a Gallade instead of a Gardevoir (or they could program it that what he ends up with depends on what gender Ralts he captures). In addition to this Wally also has a Roselia on his final team so they could also evolve that into a Roserade. WAIT! Being there are 5 fully evolved Pokemon they'll be adding, how about they give Wally all of them! He can start with a male Ralts, then as you battle him other times he'll add a Nosepass, Roselia, Duskull, and female Snorunt to his team. Some will evolve but not all the way until the final battle where Wally would reveal he has evolved them to a Gallade, Probopass, Roserade, Dusknoir, and Froslass! That would be neat, though sadly not likely, though I'd say him getting a Gallade instead of a Gardevoir does have a good chance at happening.
Roxanne: Don't worry, I'm not going to suggest for her Gym Battle she should have a Probopass, but in rematches she'll most definitely have one (she used one in BW2's Pokemon World Tournament).
Phoebe: She uses not only a Dusclops, but TWO Dusclops! She definietly needs to evolve one of them, she is a member of the Elite Four afterall. And while we're changing Pokemon, can we also replace one of her Banettes as well? Actually, let's change her team to being Dusclops (holding an Eviolite), Shedinja, Banette, Sableye, and Dusknoir. There, now she looks like a member of the Elite Four!
Glacia: Yeah, kind of a bad idea to have an Elite Four who specializes in Ice-type Pokemon even though Hoenn only had 2 Ice-type Pokemon families! Oops! So while you can replace her extra Glalie with a Froslass, that does leave her with 2 Sealeo! Hmm, maybe they can add at least one more Ice-type family to the Hoenn Dex, just so they can replace one of her Sealeo with it.

Physical-Special Split:
Each Generation changes the way you play Pokemon in other ways besides giving you new Pokemon, Moves, Abilities, and Items. Addition and changes to certain game mechanics are done each generation, and Gen IV made a HUGE one when it decided that the Category of each Move should be based on the Moves itself rather than what type it is. This was a huge change which changed the core of some Pokemon drastically, for better or for worse. Of course by now we're all used to moves being categorized based on what it is so it shouldn't effect too much, technically speaking HeartGold and SoulSilver were the first games this was done to and it really didn't change that much. Still, I'm sure now some Pokemon may get some more use now that they can rely on their stronger stat and receive STAB at the same time.

And I have to stop. Luckily we just got finished with the features I think you should be aware of from Gen IV! Next I'll go over features for Gen V and for Gen VI!

Triple & Rotational Battles:
While it'll probably only pop up in a special location, it's kind of funny how the generation that introduced us to 2 Pokemon fighting at the same time is now also going to have some place where you can have 3 Pokemon fighting in two ways. Of course Double Battles will be more prevalent, especially since one of Hoenn's Gym is a Double Battle, but just keep your eyes open and always have your first 3 Pokemon ready to battle.

(Maybe added to one of the Battle Frontier Facilities?)

TMs & HMs:
Something which no remake has yet to experience was the biggest change that Gen V's introduced: Infinite use of TMs. Now that TMs are infinite this might cause some notable differences in the ways you get some TMs (and TMs that were sold in shops will probably have their price increased).
Another thing about TMs is that, due to the change in how they work, it could be possible that Omega Ruby and Alpha Sapphire could use the TM and HM list that the original Ruby & Sapphire said. The Kanto and Johto remakes needed to have the same TMs and HMs as that generation main games since a Pokemon was able to hold TMs back then so in order for the games to be compatible they needed any item that can be held by a Pokemon to be the same (they then used Move Tutors to "replace" the TMs that were in the originals that weren't in later generations). However, though they could make the two list of TMs different they might also keep it the same as in XY. Obviously Omega Ruby and Alpha Sapphire are running off the XY engine and usually those engines have the list of TMs built in. Also it would keep things consistent between the games and provide you use of new Moves that you otherwise wouldn't have access to (thus also allowing them to put in special Move Tutors to teach the Moves that old TMs once had). Now this may not apply to HMs as in Gen III the Moves Flash, Rock Smash, and Dive were HMs which you were given when the story wanted you to have it, so it could be possible they may change the HM list to add those back in.
Speaking of story, another change that Generation V introduced was not needing Badges to use HMs... I'm going to guess for these remake that they'll be re-implementing that though. Remember, these games were built with those restrictions so it it could be difficult to write around them. Its just more simple to add back the Badge restriction then to create new reasons why you couldn't go to a location ahead of the story.

(Looks like someone needs to take a trip to Roxanne's Gym)

Elite Four Order:
Another interesting change Gen V had was that it let you battle the Elite Four in any order you wanted to. This resulted the Elite Four to have their Pokemon being the same level as each other though probably meant they were overall made more difficult. I wouldn't mind seeing them do this for the Hoenn Elite Four, as I pointed out before their teams could REALLY use a look over and adjusting. It would also give them a chance toredesign Ever Grand City and the Hoenn Pokemon League.

(Hoenn's Elite Four is Dark, Ghost, Ice, and Dragon, which one will you battle first? Last? Actually I wouldn't be surprised if many players battled them in the same order as the original for nostalgia sake)

Generation VI Features:

Fairy-Type:
Let's start off with the big one: the introduction of Fairy-types. And looking through the old Hoenn Dex the following Pokemon had been re-typed to be part Fairy-types: Jigglypuff family, Marill family, Ralts family, and Mawile. While not a lot some are notable like the Ralts Family and the Marill family (if you don't pick Mudkip as your starter). Having a Fairy-type may not be a bad idea though, two of the Elite Four's types are weak to Fairy-type, one being Dragon which Fairy-types are immune too! Of course you'll have to be careful if the Champion is Steven as Fairy-types are weak to Steel-type (except for Mawile who's part Steel-type make it neutral to Steel (and immune to Poison! Just don't put it up against a Fire- or Ground-type)) but another change may help elevate that problem. Overall, while they may not be as apparent as they were Gen VI (having their own Gym, their Champion's main Pokemon being part Fairy-type, and one of the Legendaries being Fairy-type didn't hurt), they will still be in the game in some form and could be worth the use. Speaking of the Ralts family, if Wally does become more of a rival then his main Pokemon will be part Fairy-type (whether they choose to have him use a Gardevoir or Gallade in his last battle not withstanding)!


(They're maybe only 4 families of Fairys, but they'll do their best to rock the entire Hoenn region)

+10 BST Increase:
Just thought I'd quickly mention this, some Pokemon in Gen VI got one their stats thus their BST increased by 10. Not a major change, but something you'd may like to know in case you notice some Pokemon seem a tiny bit stronger stat wise. To name a few of these Pokemon who pertain to Hoenn: Wigglytuff, Azumarill, Beautifly, Exploud, and Roserade.

(Also Pikachu got a +20 BST increase, though it only went to its defensive stats which were low and are still low)

Mega Pokemon:
In addition to Latios and Latias having Mega Stones, quite a number of Gen III Pokemon got Mega Evolutions or those in the original Hoenn Dex: Alakazam, Pinsir, Gyarados, Heracross, Blaziken, Gardevoir, Mawile, Aggron, Medicham, Manectric, Banette, & Absol. That brings up the question whether they'll introduce Mega Stones into the plot of the Hoenn games. Some are saying that the new Groudon and Kyogre forms are Mega Evolutions though I already gave my opinion of them being just new alternate forms. However if there were any Pokemon to receive new Mega Evolutions I would think it would be Sceptile and Swampert being Blaziken has a Mega Evolution. I'm sure Sceptile wouldn't mind becoming part Dragon-type and Swampert wouldn't mind more Attack for stronger Earthquakes.

(One of these things is not like the other...)

Also, once again Gardevoir comes into the discussion which is starting to make me think maybe he should keep a Gardevoir since it's not only Fairy-type but also has a Mega Evolution. That is, of course, they also give Gallade his own Mega Evolution.

(And before you say there can't be any new Mega Pokemon until next generation, XY allows for patches so I think its perfectly possible for them to introduce new Mega Evolutions and just patch them into XY. Of course will they actually do that is another story...)

Finally, if they do have Mega Evolutions in the story, no doubt Steven Stone's Aggron will Mega Evolve which may mean that may become his star Pokemon. Previously his star Pokemon was Metagross but I personally think Aggron fits him more since his name is Steven Stone (Steven =/= steel) and Aggron is a Steel- and Rock-type.

(Move over Metagross, you got competition!)

It's getting late so I'll finish up tomorrow. And then we can take a quick look over of the important characters of the game!

GYM LEADERS:

Gym Leader #1: Roxanne

Type: Rock
Title: "The Rock-Loving Honors Student"
Badge: Stone Badge

Town/City: Rustboro City, "The city probing the integration of nature and science".
RSRS-EE
Home of the Devon Corporation, I imagine that at least it will be getting a major redesign if nothing else in Rustboro City does, it is the biggest building there. After that there's really not much else to say about Rustboro City graphic wise. Maybe they could play about with that nature and science theme a bit. That fountain would be a good photo spot, especially if they made it more fancy. Or better yet, redo the front of the Devon Corporation and move the fountain there so that you can take a photo of you in front of it and the Devon Corporation.
Gym Puzzle: In Ruby & Sapphire it was just a straight walk to her unless you wanted to ignore the trainers in which case you took the very obvious paths around them. In Emerald they changed it so that it was a bit more of a maze, but not a complicated one. Actually you could still just walk right up to Roxanne if you wanted to, you'd just have to battle some trainers. And no, though the formation of the walls in the Emerald version looks like it makes an "R", that's just coincidence as Roxanne's Japanese name is Tsutsuji.
RSRS-EE
So how might they rehaul this Gym? Well I think instead of navigating around walls, we should be climbing up and down rocks, sort of like Whitney's Gym in HeartGold & SoulSilver. You could just walk straight forward to Roxanne as rock walls overshadow you and battling through the trainers who are hiding in the crevices or you can scale up the rock wall to the top where you can walk around the trainers and then climb back down right next to Roxanne. If they want to make it "challenging" they could hide the stairs/climbing wall in the first crevice you walk past so you'll need to be paying attention to see them. Might not be much, but its the first Gym, besides you have a Nosepass to worry about.
Battle: Roxanne's team are Geodudes and a Nosepass. In Ruby & Sapphire she just had one Geodude though in Emerald she was given an extra one.
Her Pokemon are very defensive. Geodude has high Defense and a decent Attack stat but has pitiful Speed and Special stats. Nosepass is a it tougher, it has a very high Defense stat and a good Special Defense though everything else is lacking (however with defense like that it'll probably last long enough to do some damage so don't take it lightly).
The Geodudes Ability are Rock Head which doesn't factor in as they know no moves which cause recoil, but Nosepass has Sturdy which lets it survive 1HKOs with 1 HP when its at full HP.
The Moves you need to watch out for is Rock Throw and Rock Tomb which they all know in Ruby & Sapphire though Nosepass only knows Rock Tomb in Emerald. Rock Throw is just a damaging Rock-type Move, but Rock Tomb will lower your Pokemon's Speed stat by 1 stage. In addition they all know Tackle just in case you brought something that resisted Rock and have a move that can increased their Pokemon's Defense stat (Defense Curl for Geodude, Harden for Nosepass). Finally in Emerald they gave Nosepass the move Block to prevent you from switching out.
Nosepass also has an Oran Berry in Emerald to heal 10 HP if it goes under 1/3 of its HP (and remember, it has Sturdy).
Obviously you'd want to use a Grass-, Water, or Fighting-type against Roxanne. If you started with Treecko or Mudkip that's easy enough, for if you started with a Torchic don't panic, there's still hope. There's a trainer in a nearby house who would trade you a Pokemon with a type advantage over Rock-types for a Pokemon you can easily catch in a previous route (in Ruby & Sapphire it was a Makuhita (who learns Arm Thrust at Level 10 back then) for a Slakoth but it was changed in Emerald to a Seedot for a Ralts (Seedot won't have an attacking Move, however it can learn Bullet Seed which TM you can get on the Route right before Rustboro City, at least back then)).

Now if they have her use three Pokemon, I'd suggest they swap out her extra Geodude with maybe one of the Gen III Fossil Pokemon. My pick would be Lileep as it's defensive but also has a good Special Attack stat, and being Grass-type it'll provide her some coverage against Water-types and a Pokemon who receives neutral damage from Grass-types. I'd also change her Geodude's Ability to Sturdy so that it has at least one chance to attack. As for Nosepass, it's pretty okay as is. Personally I would have use a Sandstorm strategy (and maybe replace the other Geodude with an Anorith to deal with Grass-types), but that may be too much of a challenge for new players (though then again, she's a Gym Leader thus SUPPOSE to be challenging).

Gym Leader #2: Brawley

Type: Fighting
Title: "A big wave in fighting"
Badge: Knuckle Badge

Town/City: Dewford Town, "A tiny island in the blue sea"
RSRS-EE
A town by the beach, they can make place look very nice in 3D. Honestly I'm more interested to see what they would do with Granite Cave.
Gym Puzzle: In the originals games it was explained that Brawley wanted to make his Gym as dark as the ocean floor to challenge trainers. The gym is a bit of a more of a complicated puzzle than Roxanne's, but not by much. Pretty much if you make a wrong turn you'll get into a trainer battle. Also after every battle the bit of light surrounding you will increase in size, though it doesn't really help that much in knowing which way to go (and if you know what path to take you'll never have to battle a single trainer). Another quick note is that in Emerald this is the first Gym to feature a double trainer battle.
RSRS-EE
. While Roxanne's Gym will probably get a re-imagining, I think they might give Brawley a new Gym Puzzle (which they did with some Gym Leader is HeartGold & SoulSilver). But to what I have no idea. He's a Fighting-type Gym Leader yet he's a surfer dude (meanwhile in Sinnoh we have a Gym Leader who's a Mexican wrestler that trains Water-types...), that doesn't really leave much to the imagination. Infact I wouldn't be surprised if they initially gave him this puzzle because they couldn't think anything else for him. Maybe use the puzzle for Marlon's Gym in Black 2 & White 2 except instead of lilypads make them surfboards and in order to proceed through the Gym you need to smash through barriers by having the surfboard climb a wave which will give the surfboard enough momentum to do so. And then scatter a few trainers here an there (or you could make it that you have to challenge the trainers to make the waves appear). It would give a Gym an interesting visual for 3D at the very least.
OR, they could use this blackout idea and use the Glittering Cave's gimmick, that would work too.
Battle: Being a Fighting-type Gym Leader, Brawley's Pokemon are offensive powerhouses. In Ruby & Sapphire he use a Machomp and Makuhita but in Emerald they added a Meditite to his team.
Machop and Makuhita are similar as they have high Attack and decent HP, but have low stats everywhere else. His Meditite offers a bit of a mix-up as its not only his fastest Pokemon (and at this point in the game might be even faster than your Pokemon) but also has higher defensive stats and its offensive stats are even so it can be a mixed attacker (at least looking at its stats alone... we'll get more into that with its Ability). However Meditite has balanced stats meaning all of its stats are barely edging on acceptable (once again, at least looking at its stats alone... let's move onto Ability now).
Machop and Makuhita have Guts, so don't give them a status ailment or else they'll start bringing the pain! However Meditite can start bringing the pain right away as it has the Ability Pure Power which doubles its meh Attack stat to Machop's level (and remember, its faster then Machop)!
As for Moves, this is where Brawley become a joke if you know how to mess with him. All of his Pokemon's attacking Moves are FIGHTING-type, meaning if you have a Ghost-type he can't even touch you! Well, if you're playing Emerald, while you'd still be able to mess with his Machop his Makuhita at least knew Knock-Off in Ruby & Sapphire which even have it some type coverage (as well at got rid of your Pokemon's item)! I don't know why they changed it, but it they don't change it back know you now how to mess with Brawley. Anyway all his Pokemon know Bulk Up which will make them physical powerhouses so watch out for that! Machop can use Leer to lower your Pokemon's Defense or just start attacking with Karate Chop or its other offensive move. In - it was Seismic Toss (does direct damage equal to Machop's level which was 17, low but can still be a threat at this point in the game) and in Emerald it was Low Kick (does damage depending on your Pokemon's weight, the heaver your Pokemon the more damage it'll do). Meditite will probably try setting up Light Screen and Reflect to give Brawley's Pokemon some defense, however its only attacking move is Focus Punch so as long as you keep attacking it there's nothing to worry about. Finally Makuhita acted differently depending which version you were playing. In Ruby & Sapphire Makuhita knew Knock Off and Sand-Attack, so it was most likely to get rid of your item and/or decrease your accuracy. But in Emerald those moves were changed for Vital Throw (a strong move that goes last but is guaranteed to hit (unless you were a Ghost-type)) and Reversal (which did more damage the less HP Makuhita has). However Makuhita's most dangerous move it knew in both versions: Arm Thrust. It's a multi-hitting Move which racks up damage real fast, possibly even knocking out your Pokemon with one use.
If that's not bad enough, Makuita has a Sitrus Berry in Emerald to heal back 1/4 of its max HP when it goes under 1/3.
You probably have a Flying-type or Psychic-type Pokemon by now, use that. Actually as long as none of your Pokemon were weak to Fighting you could probably take one hit if you play carefully. And if you had a Ghost and are playing Emerald, pretty much auto-win.

Brawley's team is fine, but their Moves need MAJOR work. First off, you can now replace Bulk Up with Power-Up Punch, that extra Defense boost wasn't really doing anything. Starting with Machop I'd replace Seismic Toss/Low Kick with Smack Down to give those pesky Flying-types some trouble (and to be able to hit Ghost-types). Now having Power-Up Punch, Meditite can replace Focus Punch with a Psychic-type Move. Sadly the only Physical Psychic Move it learns is Psycho Cut via an Egg Move, so it might have to just use Confusion. As for Makuhita, I'd give it back Knock Off to deal with Psychic- and Ghost-types. Personally, I'd also give them some moves to handle Fairy-types but those moves are either too strong (like Poison Jab) or are Egg Moves (like Bullet Punch) so if you can get a Fairy-type it might not be a bad idea.

That's two Gym Leaders down, but I got to so but next post we'll continue with the rest... or at least as many as I can.

Gym Leader #3: Wattson

Type: Electric
Title: "The cheerfully electrifying man!"
Badge: Dynamo Badge

Town/City: Mauville City, "The bright and shiny city of fun!"

Above: Ruby & Sapphire
Below: Emerald

Mauville City is actually the center of Hoenn, so I'm hoping they they give it a Castelia City/Lumiose City and make it into an actual city. I'm curious what they'll do with the Game Corner, sadly the slots are gone but what are they going to replace it with? Voltorb Flip? Also maybe they could do something with bikes since this is where the bike shop is (maybe add in a courses for the Acro and Mach Bike somewhere?). And let's not forget New Mauville, now that place would probably look really interesting, especially if the really hone in on the electricity theme.
Gym Puzzle: Electric poles are creating electric gates, you need to press the switch to change around the electric gates until you clear a path to Wattson. It's a pretty straight forward puzzle, pretty much after pressing on a switch you go to the next one you didn't press on yet. However this is the first Gym with unavoidable trainers.
RSRS-EE
While I think the theme is here, though I think it needs to be spanned upon. I like the idea of electric gates and needing to go find a switch to change around the gates, but as of right now the puzzle is just too simple. Maybe increase the side of the grid, require the player to having to go back and hit a switch they already did, and I think you'll have a pretty good and visual Gym Puzzle.
Battle: Be it Ruby & Sapphire or Emerald, Wattson's team has a bit of a problem. It's not as bad as some teams we'll be getting to, but in - he had both Magnemite and Magneton as well as a Voltorb (and no Gen III Pokemon!). Thankfully his Emerald team fixed this by getting rid of the Magnemite and giving him two Gen III Pokemon, the problem is they're part of the same evolutionary family: Electrike and Manectric! Either way, I hope you brought Paralyze Heals and something that can take Special attacks.
The Magnemite family has very high Special Attack and good Defense, and though Magnemite's other stats fall short, Magneton's other stats are decent enough to make it a challenge. Voltorb is very fast... and that's about it or it. It'll probably attack first, but that's all it'll be doing, especially if it decides to leave with a bang. Finally the Electrike family has high Special Attack and high Speed, well, if you're Manectric. Electrike's Special Attack and Speed are passable with its other stats being subpar, however Manectric is what you have to watch out with a high Special Attack, Speed faster than Voltorb's, and decent in its other stats.
The Magnemite family have the Ability Magnet Pull which prevents Steel-type from switching out, a type you really shouldn't be using in an Electric-type Gym anyway. Voltorb is interesting as in Ruby & Sapphire it has Static which can paralyze the opponent that makes contact with it but in Emerald it has Soundproof which makes it immune to Sound-based Moves. Both are handy Moves, though I think it makes most use out of Static. Lesson: Don't use Physical attacks in an Electric-type Gym. And don't think you're safe from Static in Emerald as the Electrike family has it as their Ability.
The Magnemite family all have the same Moves no matter what evolution stage or version. Well, not all the same, Magnemites main attacking Move is Thundershock while both versions Magneton's main attacking move is Shock Wave. However their other 3 moves are the same: Supersonic (yup, Wattson also used a Confusion strategy), Thunder Wave (Fun Fact: In the metagame the combination of Paralyzing and Confusing a Pokemon is called "Parafusion"), and SonicBoom (which, depending on the being, could actually be more dangerous then its main attacking move as it always does 20 HP of damage). So yeah, the Magnemite's family's job looks to be both paralyzing and confusing your Pokemon while doing some sure damage with Shock Wave (that never misses) or SonicBoom (probably for those pesky Ground-types). Between the version Voltorb only shares two moves, Spark (main attacking Move in Ruby & Sapphire) and Selfdestruct (because of course Voltorb explodes). However in Voltorb Ruby & Sapphire knows Charge as to power-up its only Electric-type move (meaning if you have the Ground-type all you need to worry about Voltorb is it Selfdestructing) and Screech (which decreases your Defense stat by two levels... in a Gym who's Pokemon only use Special moves...). In - they changed those Moves to Rollout (even though its Attack stats is its lowest stats and it's not really covering any weakness) and Shock Wave (though Spark, which was still considered a Special Attack back then, was stronger so it'd probably still use Spark which has a high chance of causing Paralysis). Finally the Electrike family had the same deal as the Magnemite family with their moves. Electrike and Manectric know Quick Attack (for some free damage I guess, though it's not really helping them much), Howl (which increases thier... Attack... well I guess it sort of helps Quick Attack) and Shock Wave. However Electrike has Leer (which decreases... Defense...) while Manectric has Thunder Wave just incase you thought to save a Pokemon for it that wasn't Paralyzed.
Finally, Manectric has a Sitrus Berry.
Well, you can pretty much wreck this Gym with a Ground-type, just watch out for Confusion and SelfDestruct though. You can try to plow through this Gym with another type (preferably not weak to Electric-types), but it'll be susceptible to Paralysis and no matter how many times you'll heal it Wattson will probably just inflict it on it again, probably even get to move first!

Assuming their giving him 4 Pokemon, toss the Electrike and get a Plusle or Minun. Why a Plusle or Minun? Because its a Gen III Pokemon. For Voltorb, give back its Static Ability, replace Rollout with SonicBoom and replace Spark with Thunder Wave and we're all good. For Magneton give it the Sturdy Ability. And for Manectric, I can see the problem with it, it doesn't really learn any Special Attack but a lot of Physical. However it does get Electric Terrain so I suggest replacing Howl with that. Finally, I'd say replace Quick Attack with Snarl, its a decent Special Dark-type move it can learn by TM and lowers the opponent Special Attack by 1 stage. If they really want to shake things up, I would actually make Wattson do a Double Battle and replace Voltorb and Eletrike with both Minun and Plusle. I'd also give Manectric Ice Fang (one of its Egg Moves) just for Ground-types. Though still, even then a Ground-type would probably still wreck the place.

Gym Leader #4: Flannery

Type: Fire
Title: "One with a fiery passion that burns!"
Badge: Heat Badge

Town/City: Lavaridge Town, "An excellent place for relaxing!"
RSRS-EE
Now this entire area I can't wait to see in 3D! Honestly I'm more curious to see what they'll do with the cable car scene of going up Mt. Chimney, however with Lavaridge suppose to be a town famous for its hot springs I can see them redoing the entire place and making it into a resort hotel with hot spring baths!
Gym Puzzle: A "teleporter" puzzle of shorts. The Gym is a sauna and to get to Flannery you'll need to jump down the holes to the basement. These holes are actually geyser springs, one which you'll need to shoot you back up to the first floor where you'll hopefully have progressed to the next room. Jump down the wrong hole and you'll have to start from the beginning. Eventually you'll find the right geysers that lead to Flannery. But be vigilant! Not only are trainers all around but some are hiding in the pools the geysers come from and will challenge you upon approaching!

Above: Ruby & Sapphire
Left: First Floor - Right: Basement
Below: Emerald

Like Wattson's Gym, I think this Gym Puzzle only needs a slight redesign and it'll be good. They can also make the shooting up the geyser look cool with the right camera angle.
Battle: Flanney has a Sunny Day Team! However she has double problems as well, Ruby & Sapphire has her with two Slugma while Emerald has gotten rid of a Slugma but given her both members of the Numel family! Though surprisingly you don't need as much Burn Heal as you think you would.
Slugma has decent Special Attack but that's it, other stats are low with Speed being its lowest. Numel family are offensive Pokemon with high Attack and Special Attack with decent stats everywhere else except Speed which is low. Obviously this applies more to Camerupt than Numel who has barely acceptable Attack and Special Attack to say the most about it. Finally her signature Pokemon, Torkoal has very high Defense, good Attack and Special Attack, and low Speed. Flannery Pokemon aren't very fast but her strongest Pokemon are a few tricks up their sleeve.
All her Slugma have Magma Armor which means they can't be Frozen, in other words a useless Ability and she only be used when trying to hatch eggs outside of battle. Numel has Oblivious which means it can't be infatuated like you would have tried. Camerupt... also has Magma Armor! Finally Torkoal has White Smoke which prevents stat decreases though only if afflicted by the opponent, thus just as useless as her Pokemon's Abilities.
While Flannery's Pokemon lack in Abilities they make up for in Moves! Shockingly her Slugma only share two moves with other other: Light Screen and Sunny Day. The Slugma that only appears in Ruby & Sapphire knows the classic Flamethrower and and Rock Slide (which would have been more useful to it if it was evolved).The other Slugma appears in both versions and its other two moves are Overheat as its main offensive Move and Smog as a sneaky Poisoning Move so don't underestimate it! Numel also knows Overheat and Sunny Day but also has Take Down or serious Normal-type damage and Magnitude which could be rather painful if you brought any Rock-type Pokemon. Oddly her Camerupt seems like a bit of a downgrade, it too knows Overheat and Sunny Day while its other moves are Tackle and Attract (Attract is another gimmick of Flannery, and if you have a male Pokemon it can rather be annoying so bring in a female Pokemon if you can). It's like they switched Numel and Camerupt's moveset. And Anyway, finally her Torkoal is mostly same in both versions sharing the moves Overheat, Body Slam, and Attract. However in Ruby & Sapphire her Torkoal knew Flail (which could be quite powerful if you were attacking her physically thus chipping away at its HP) while in Emerald it knows Sunny Day to keep up that sun support.
Finally Torkoal has a White Herb which prevents any status decrease done, including to itself. In other words, she can use Overheat at full power two times! And after the 2nd time she still has a perfectly good Attack stat to use Body Slam (which can possibly Paralyze, by the way)!
Best bet to beat Flannery is bringing in a female Water- or Ground-type Pokemon. Otherwise you may have some problems, especially if your Pokemon is male. Her Pokemon are slow but HIT HARD and her strongest ones can take quite the beating too.

Assuming they're using Emerald team. First thing first, get rid of Numel and get a Ninetales (you have plenty of Gen III Pokemon, you're allowed at lest one previous generation Pokemon). With that done, evolve that Slugma to a Magcargo and replace its Ability Magma Armor with Flame Body and the Move Smog with Rock Slide. For Camerupt, I say give replace its Ability Magma Armor with Solid Rock and give it Numel's moveset! Finally Torkoal is actually okay as is. However, if I was deciding things, being their Fire-types on a Sunny Day team I would have give at least one of them SolarBeam.

And it's getting late where I am so sadly I must stop again. However I don't think 2 Gym Leaders per post is bad pacing. So next time we cover Gym Leader #5 and 6!