Interesting that you post this because I had a kind of similar idea a day or two back, although that was more along the lines of all the humans disappearing and the Pokemon making their own society.

Anyway, a few questions:

1) How do trainers have Pokemon if there aren't a lot of them around? Do they just get lucky and find them or something?
2) Is this area separate from the rest of the world? Meaning, do places like Kanto and Hoenn exist, and if so are they in a post-apocalyptic state as well or are they functioning as well as ever?

Besides this, the idea I have so far is for a talking Pokemon of some kind, perhaps a mutant due to the environment. Would that be acceptable to RP as?