about the evil team sprites, why don't you remake team rocket and make flashes instead of the "R"'s? i think it's a funny idea xD and your maps look totally amazing, really they're so great!
btw, i got an idea for the starters: i think eevee is a good choice, but why don't we insert glaceon in the game? and then we could edit the evolution of eevee, then we could give the player in every region a new eeveelution (funny word xD). because if you simple start with an eevee and then one time give the player a waterstone, you could also evolve your eevee to espeon or umbreon and the two are a little bit out of story, isn't it so?
or second idea: you edit the evolution, so it could not evolve to espeon or umbreon and on one time you give the player the choice: which of the elements do you prefer? and then ypu could choose between waterstone, firestone and flashstone (or whoever the yellow stone is called xD)
what do you think?