i have the best idea ever , might not work though, the player changes into a pokemon when you go into some dungeons like mystery dungeon and Zelda:twilight Princess!!!!!!!!!!!!!
for this you could make another sprite for the trainer and make it change when he/she goes in but you cant use any pokemon and wild pokemon dont attack you anymore , they talk to you!!!!!!!!!!!!!!!!!!!!
and they would call you the Twilight Trainer! haha sweet!
and the pokemon should be a poochineya i mean like a wolf thing
i dont know it can be any thing you , the maker of the game want or you could give them a choice like sb in the game asks them which one they like the most " pokemonname1, pokemonname2, pokemonname3 " and then change to the selected pokemon when they go into that dungeon!