Right so.. theory time.
He's named "Pokemon Trainer" because his other costumes turn him into other trainers, other trainers might have different Pokemon with movesets that act the same way, but have altered graphics to fit the type. Like the clones in Melee?
The fact that Pokemon only come in a set color would and 4 PT's would make things very confusing, might help this theory.
PT likely stands on some sort of floating platform to move long with floating/moving stages, in storymode, where there seem to be more solid backgrounds, he might be set up near the camera, and throw his pokeballs from the screen.
Squirtle is likely a fast damage racking character, but is light, and has poor recovery. When Squirtle gets tired and damaged, the PT switches to Ivysaur, who is slower, and possibly does less damage, but is heavier and has better recovery by using his vines like Samus' grappling beam. Finally, at high percent, the PT switches to Charizard, who owns the KO moves needed to finish off the by then hopefully highly damaged opponents, is quite heavy, and can use his wings for long comebacks, which is needed, since the PT's overall percentage should be pretty high by that time. Charizard will however be missing combo ability due to his slowness, making him poor at doing damage.
Obviously, the challenge when player as the PT, will be that if you fail to do enough damage with Squirtle before he gets tired, eventually Charizard will be having himself a hard time finishing off the opponents. The plus side to the PT would be that if all goes well, he'll always have the right type of character for both early, mid and late game.
I thus predict that optimally, there should be 3 Pokemon switches taking place per stock, this means a lot of switching, so switching shouldn't take a lot of time.
Erm, yeah, that'll do for now.
