I was playing Black/White 2 and was doing the movie "Timegate Travelers" which for those who aren't familiar with it, is a movie about a scientist who travels to the future in which Bug Pokemon have become anthropomorphic and have taken over the world enslaving humans making "them" fight each-other.
This is one of the more interesting story concepts I have ever seen in Pokemon. And yes I know it's a spoof off of Planet of the Apes, but still this idea could be used in some way. Heck, Gamefreak could make a game just with anthropomorphic Pokemon living like humans, similar to PMD but more modern with TV and videogames and schools and stuff like that. (Though I don't know how the game mechanics would work, maybe a visual novel or an Earthbound like RPG?)
Maybe I'm getting carried away, but it does sound fun.