Reading through the thread, I can definitely tell we're going in different directions here. I like some of the ideas presented, but others just don't jive with me.
For example, I'm not a fan of the idea with the trainer and pokemon meshed together as race and class. The way I've done it, the human (player) and pokemon (monster) are two separate entities entirely, with their own racial features, class abilities, and feats. In fact, a human doesn't even need to own any Pokemon to play, though they'd obviously get left out when everyone else is battling a gym leader or something.
Also, having each Pokemon count as a seperate class just isn't going to work. You'll die of old age long before you accomplish that lofty goal. Here are some of my suggestions:
1) Design 17 Pokemon classes, one for each type, and create their at-will, encounter, and daily powers based on the video-game moves of that type
or Design only one Pokemon class and have each type a different school, much like a Wizard.
2) The second and third evolutions of a Pokemon become their Paragon Path and Epic Destiny, respectively. Again, it would probably be best to base these around type (Fire, Grass, Bug, etc) rather than individual species.
3) Humans should start out with a base class, then gain a prestige class at 11th and a destiny at 21st. The ones you've invented work fine. Personally I went with Trainer, Breeder, Coordinator, etc as base and then did Professor, Ranger, etc as Paragon paths. We basically had the same ideas for Epic Destinies.
4) Humans should gain talents, cheers, and other powers related to raising, battling, and finding/catching Pokemon. Humans could also gain a few Pokemon moves with multiclass feats (remember there are Human Psychics and martial artists).
Your class skill selection looks good. I chose many of the same things. However, I would definitely have both humans and pokemon have their own skills. Pokemon can at least have basic things like Athletics, Perception, and Stealth. I also really like this:
Quick idea for capturing: you make an attack against each of the Pokemon's defenses. The attack is base d20 + one-half trainer's level. If the Pokemon is at full health, you need to hit all three defenses to capture it. If the Pokemon is injured (at half health), you need to hit two defenses. If the Pokemon is at one-fourth health, you need to hit one defense. The Pokeball used gives certain bonuses depending on its type, and you get normal bonuses from the target Pokemon being helpless (from sleep or frozen) or having combat advantage.
How does that sound?
I have yet to fully develop my capture mechanic yet, and your idea looks excellent. If I steal it I'll be sure to give credit where its due.

I did have the idea to have different Poke Balls add a bonus on the roll. In addition to the Great and Ultra, you also have the dozens of others like the Net and Timer Ball, which provide bonuses in more specific situations.
note: Ack! Bulbapedia is apparently updating their site, and since all my images are from there my site is looking very not good.
