Okay, I decided to look around a bit and found out from Bulbapedia that there will be a new feature to HeartGold and SoulSilver that wasn't in any games before, so I thought I would bring that up as no one have mentioned it yet.
Here are my guesses:
A. Being we were able to catch Lugia and Ho-Oh (along with the Beast Trio; Entei, Raikou, and Suicune) in Gold, Silver, and Crystal then I think it's a pretty much garuntee that we'll be able to catch them in the game without need of a Nintendo Event (though we'll probably need a storyline event which will occure while playing the game).
However I think a better question to ask here would be "Will they allow us to catch both Lugia and Ho-Oh in each game?". In both Gold and Silver, you were able to catch both of them without needing to trade with the other game. For Lugia you needed the Silver Wing and then go to the Whirl Islands while for Ho-Oh you needed to have the Rainbow Wing and go to the Tin Tower in Ecruteak City (albeit they were at different levels (with the one featured on the boxart being met up with first and at a lower level) depending which game you were playing but both were still catchable in either version). Now being that starting with Generation III the Legendary Pokemon that is featured on its respected version is the only Legendary of that duo that could be caught (you would need the other paired version to get the other Legendary or wait till the third version of that generation to come out).
B. Well we were told about that new featured never before seen in a Pokemon game to look forward too, and also there are the "features" which only Gold and Silver had that didn't appear later on which I'll get to in a second. Finally I'm sure the storyline has been revamped in someways like they did for FireRed and LeafGreen. And of course, I'm sure many (or at least me) are curious what those "badges" in the game logo are for.
C. They'll probably make a Regional Dex for Johto and then after you complete the game and see all the Pokemon in Johto it'll get upgraded to the National Dex like in later games. Don't forget, in FireRed and LeafGreen, even if you did what was required for a Pokemon that has another Generation Evolution to evolve (Like Golbat into Crobat), it wouldn't allow the Pokemon to evolve until you got the Ruby and Sapphire item and used them to allow trading capabilities with Ruby, Sapphire, and Emerald.
Now with that done, I have a few things I'm wondering about that I think I should share:
1. Apricorn Poke Balls - One ofthe most interesting features in Generation II was that you can have Kurt make a Apricorn Poke Ball out of different Apricorns you bring him. Now the thing is, Apricorn Poke Balls do not appear Generation III or IV games, not even hidden in the game's data like the "Johto" location for a Pokemon's in-depth status screen. They surely can't leave out this feature, so there are only a few things I can see them doing to "fix" this:
A.) Have the Apricorns change into Pokeballs that are in later Generation games. To be perfectly honest, the Apricorn Poke Balls aren't all that great. In addition to that many of them seem to have "replacements" in later Generations (The Lure Ball is "replaced" by the Net Ball and Dive Ball, Level Ball "replaced" by Net Ball, Friend Ball "replaced" by Luxary Ball, Fast Ball "replaced" by Quick Ball, etc.). It wouldn't be too hard to change around which Apricorn can become which Poke Ball, and the newer generation Poke Balls are much more useful then the Apricorn Poke Balls anyway.
B.) Keep the Apricorn Balls as they are and if you want to trade over to Diamond, Pearl, or Platinum you'll first have to see someone who could put Pokemon into different Poke Balls. Now they can either program it so that the Pokemon in the Apricorn Poke Ball goes into a normal Poke Ball or you can choose which kind of Poke Ball you want the Pokemon to go in. But eitherway this feature will allow the Apricorn Poke Balls to exist and allow trade to Diamond, Pearl, and Platinum.
2. GS Ball and Celebi - Speaking of Poke Balls, how can we forget about the very plot device in the anime to get Ash and co. to go to Johto: the GS Ball. As well all know, in Gold, Silver, and Crystal we only had the GS Ball for like one or two towns and afterwords Kurt takes it and we never hear about ti again. Though in Japan another GS Ball could be downloaded using a mobile phone into their Gold, Silver, or Crystal version and, placing it on the Shrine in the Ilex Forest, it would summon a Level 30 Celebi to be battled (and caught). But with Generation II coming a second time around, what will become the fate of the GS Ball this time? In addition, besides from past Nintendo Events, a genuine Celebi is hard to come by. Now I'm sure they'll also have a Celebi giveaway (they might even have one to celebrate the release of HeartGold and SoulSilver), but it would be nice to have the GS Ball and the shrine in Ilex Forest to serve its purpose.
3. Gym Puzzles - Now while the Gym Puzzles in FireRed and LeafGreen weren't changed, I think the puzzles for the 2nd Generation could use a bit more fixing up, especially with the graphics capability of the Nintendo DS.
4. Poke Gear - Can you imagine the fun programmers will have with this thing, especially now with the Poketch Applications and thew fact you can get and make phone calls with it?
5. Kanto... Or How About Orange Islands?... Or Both! - You know, besides from the fanmade Pokemon Naranja version, no Pokemon game ever took you to the Orange Islands even though the Sevii Islands are located further away from Kanto and Johto. So I got to thinking, being that we now have the Battle Frontier idea, why not use it to have one so that both Kanto and Johto can officially have one (they'll have to share though). And who would make better Frontier Brains then the Orange Crew? Between you and me, I even made my own title and what there battle facility would be if they were to be included in a game:
Frontier Brain (& Title) - Battle Facility - Reward
Beach Kahuna Cissy - Battle Beach - Coral-Eye
Mountain Journymen Danny - Battle Mountain - Sea-Ruby
River Capitan Rudy - Battle River - Spike-Shell
Hotel Heiress Luana - Battle Hotel - Jade-Star
Stadium Champ Drake - Battle Stadium - ????
A bit much maybe, but you get the main idea. I think they should include the Orange Islands, evenif they have to drop a large part of Kanto (though it would be great if they could fit both in, I'm sure the DS catridge has enough room.
6. Crystal Additions - I'm hoping that the additions added to Crystal will be incorporated. Mainly I would like to see Eusine who battles you every so often and Suicune appearing at certain points like it did in Crystal.
7. More About Silver - Is he Giovanni's son in other media's other then the manga? We need answers and this woudl be the perfect game to do it in!
8. DSi Feature - Surely they can work in a feature with the DSi (the game will still play on the normal DS, but you won't be able to access certain features which uses the DSi's camera)?
Well other then that I'm wondered out. I'll be here waiting for artwork (especially the new stock art for the out of place looking Generation II Pokemon), Screenshots, and gameplay.
LOL... I just realized something, do you know how many Shiny Gyarados' there will be? 
3. Updated Pokemon artowrk