I really, really like this idea!
At least, I like this idea as I'm picturing it. And it sounds like almost everyone has a different idea of how "Pokemon-based Pathfinder setting" would play out. Let me see if I can clarify this with a question:
Which part(s) of Pokemon would you put into Pathfinder?
-Is it the combat mechanics? (Fighting mainly with familiars and summoned creatures, possibly with a "capturing" mechanic)
-Is it the ecology/natural world? (Very few "normal" animals, mostly magical beasts/outsiders/elementals, each with at least one supernatural ability)
-Is it the society/cities? (Few cities, spaced far apart, separated by terrain that is difficult to traverse, monster-infested, or usually both, yet still maintain vibrant and thriving economies)
-Is it some mix of the above?
There are a lot of parts to Pokemon, and a lot of parts to Pathfinder. Which parts do you want to replace with which?