I remember back in the day when someone made some fake box art for Pokémon versions Purple and Black, where you got to play as a member of Team Rocket and collect pokémon by stealing them. Those were the days, eh? Anyway, that's kind of been done now, with the gamecube games, but in some ways I'd still like to see a pokémon game where you play as a 'bad' trainer.
So:
Purple - Arbok
Black - Mightyena
And, just for kicks, though it pains me to type:
Lavender - Igglybuff
Periwinkle - Azurill
Where you play as if you're in the girlified shoujo manga version of pokémon, where everyone is nice and there's cakes and tea every day. Also, there's no battling, just contests. I could see it being sort of fun.*
*(insert hysterical laughter here)