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Probably not, actually being Alder wanders around I wouldn't be surprised of his wife had passed away. Then again, in the Pokemon World, it seems like the social norm for trainers to be away from their family for long periods of time, be them a child, spouse, or parent.

More like, why is he carrying a machete? Weapons in my Pokemon games?

More like, why is he carrying a machete? Weapons in my Pokemon games?

This is getting a bit off topic so I'll just finish off this thought.

Ninja Skills:
Cut (karate chop, though technically ninjitsu is the martial arts of guerrilla warfare and espionage)
Rock Smash (karate chop, again)
Strength (meditate for a short while to build focus which you then transfer into strength)
Surf (as you said, running on water, though ninja's were also pretty good swimmers and can hold their breathes for a long time)
Waterfall (climbing it, as you said once again)
Fly (ninja teleport? Shadow Triad can do it, why not you?)
Flash (you'd already have improved vision in the dark (not to mention your other senses will also be heightened))
Whirlpool (same as surf, either run across it or go into a meditative state when swimming into it and use the focus to guide yourself to the other side)
Dive (as I mentioned, ninjas were good swimmers and could hold their breathes for a long time)
Defog (like with Flash, your vision would be good enough to see through the fog (and your other senses are heightened))
Rock Climb (just like with Waterfall, though probably easier here then there)

Of course this is just going by physical means and not helped by any equipment. If you were using ninja tools then you could use a sickle for Cut, a grappling hook for both Waterfall and Rock Climb, a hidden back hand glider to Fly, maybe a gunpowder flashbang/flare for Flash, and a fan to Defog. Though speaking of items I always thought for a few certain HMs it would probably be more useful most of the time to use an item instead of having a Pokemon with that certain HM.

Items:
Cut (maybe follow Banjirou's logic and carry a machete, though being how thin the "trees" are that you cut you could probably also make due with a pocket knife)
Surf (not really an item, our character just needs to learn how to swim)
Flash (a flashlight would be very easier, and we know they exist since Police Officers use them and the Hearthome's Gym Puzzle in Platinum had you using one. Heck, maybe even night vision goggles)
Dive (like above, learn to swim but also have an air tank or some kind of breathing device... actually we should probably have one of those already unless our Pokemon is somehow providing us with air...)
Defog (going with the night vision goggles idea for Flash, maybe having something like inferred or heat vision goggles)

Can't really think of any items that can help with Rock Smash, Strength, Waterfall, Fly, Whirlpool, and Rock Climb that is easy to carry around (if I had to pick, a hammer/mallet/jackhammer for Rock Smash, high tension piston/power gauntlets for Strength, grappling hook for both Waterfall and Rock Climb, ninja hand glider/jetpack for Fly, and maybe a sturdy, inflatable boat for Whirlpool (which would also be used to Surf)).

And to finish things off:

Cut (it's a thin tree in the way and we're a kid, why can't we just slip around it? Or if it's still too wide, why can't we use a big Pokemon to tear it out, a Poison-type to melt corrode it away with poison/acid, Ground-type to move the dirt under it so it's out of our way, Bug-type to eat it, Ghost-type to phase us through it, Fire-type to burn it, Grass-type to control it and move it out of the way, Psychic-type to move it out of the way with it's mind, or an Ice-type to freeze and shatter it? Why can't Pokemon like Scyther, Scizor, Kabutops, Gallade, Pinsir, Kingler, or Crawdaunt use their blades or pincers to cut it down without knowing the HM? Why can't other "cutting" moves like Slash, Night Slash, Psycho Cut, or Leaf Blade be used just like Cut?)
Rock Smash (why can't we just climb over the rock, it doesn't look like it's that big. If for some reason we can't climb over it why can't we use any Fighting-, Ground-, Rock-, or Steel-type be used to smash it into bits? Or maybe a Ground-, Psychic-, or Grass-type to user their powers to move it out of the way? Or a Ghost-type to phase us through it? Actually I'm sure any move from a strong Pokemon might be able to shatter stone)
Strength (just to tell you, a lot of these arguments are going to involve "big" Pokemon. Assuming we can't just climb over the boulder, why can't we use any big Pokemon to simply push the boulder? Have Ground-, Psychic-, or Grass-type to user their powers to move it out of the way? Or a Ghost-type to phase us through it?)
Surf (I'll skip mentioning about learning to swim since I said that above. Shouldn't any big Water-type Pokemon be able to carry us without having to know Surf?)
Fly (like with Surf, shouldn't a big Flying-type (or any big Pokemon with wings) be able to carry us without having to know Fly?)
Flash (there's a few Pokemon who can natural generate light like Umbreon, Ampharos, Volbeat, Illumise, and Watchog. Also I'm sure an Electric- and Fire-type can light the way by just using their power (heck, many Fire-types have an open flame on their body, infact I remember seeing some episodes where a Charmander used its tail like a torch)
Defog (can't any Pokemon with wings just flap hard enough to blow away the fog? Isn't that what almost all the Special Flying-type moves do anyway?)

I didn't include Waterfall, Whirlpool, Dive, or Rock Climb because with those I can see the Pokemon needing some skills to use (then again why can't I just use Fly (or a big Pokemon with wings that can fly according to my arguement) to reach the place I would use Waterfall/Rock Climb to reach and skip over the whirlpool I'd need Whirlpool to normally pass?).

And incase anyone says anything, yes, I know Cut, Strength, Flash, and Rock Climb are Normal-type moves, Rock Smash is a Fighting-type, Surf, Waterfall, Whirlpool, and Dive are Water-type, and Fly and Defog are Flying-type. I just color-coded them this way to give each one a bit more individuality instead of sharing a color with another move (except for Rock Smash which is the only Fighting-type HM).

Honestly they sort of threw the Pokemon World Tournament quickly together in terms of the previous region Gym Leaders/Champions. The only thing they worked on was new sprites for the over world, new sprites for the Hoenn Gym Leader/Champions, and their teams. Thus why they have Giovanni representing Viridian Gym (they had his sprite and wanted Blue to be counted as a Champion) and there's no Koga since, despite him being a former Gym Leader and a sprite in HGSS, he was an Elite Four member which they for some reason didn't want to include.

Also Agatha was an Elite Four member (for Indigo Plateau, to be precise), not a Champion.

Localization Name Game:
As I predicted, with the games coming out in less then the month we have a stream of names coming in:

1. Black Skyscraper and White Tree Hollow have been renamed, Black Tower and White Treehollow, respectively. As you may have guessed, these are locations in the version exclusive locations Black City (Black 2, has Black Tower) and White Forest (White 2, has White Treehollow). Within both areas you'll progress through 9 areas, each containing a battles, until you reach the 10th where the "boss" is. When you do this the first time the "boss" will be Alder's grandson, Banjirou, though going through a second time will be a Veteran trainer of equal challenge. Upon completing each area you'll be rewarded with a prize. Click the following links for more information: Black City (specifically trainer list), White Forest (specifically trainer list), Black Tower/White Treehollow (specifically boss information and prize list).

Do you ever feel small?

2. Floccesy Ranch and Virbank Complex keep their names (sort of, Virbank Complex in Japan was known as "Virbank Industrial Complex"). Floccesy Ranch is a location connected to Route 20 where you have the 2nd battle with your Rival, Hugh, and as well is the first location where you can find a Hidden Grotto. Virbank Complex is connected to Virbank City though doesn't have anything noteworthy.

You know, being both areas are probably private property, you'd think you'll get in trouble for trespassing.