Pokémon Trainer should be kept for sure but when he has a different color scheme, he changes into a new character along with a new set of Staters. Here's what I mean:
Red color scheme: Red, Squirtle, Ivysaur, Charizard
Blue color scheme: Blue, Bulbasaur, Charmeleon, Blastoise
Green color scheme: Leaf/Green, Charmander, Wartortle, Venusaur
Yellow color scheme: Gold, Chikorita, Craconaw, Typhlosion
Light Blue color scheme: Diamond, Turtwig, Monferno, Empoleon
Black color scheme: Black, Oshawott, Servine, Emboar
That does seem like a good idea. On paper. In reality, I don't think the developers would waste their time making movesets for 20 Pokemon.
It has been said SSB4 will; one, limit the amount of new characters, and two, spend more time balancing all the characters. Your idea fills up no more spots in the roster and is fine regarding statement one, but creating 20 Pokemon movesets and balancing them all would waste too much time and be overkill in regards of having more than quadruple of the appropriate maximum playable characters a series should contain.