I like Morzone's idea as a starting point, but I confess that I think it would be more interesting with a general "alliance" sort of theme. Instead of just "a whole bunch of grunts" it would be "a bunch of people from different groups getting together and allying, with probably different but ultimately compatible goals." It would give much more diversity of characters that can play around in that playground while simultaneously sidestepping the whole "what are team rocket et al doing in a Pokémon only world?" thing.