If you’re not aware, there’s already a pretty decently written fan-made Pokémon RPG called ‘Pokémon Tabletop Adventures’, that has stats for Pokémon up to Gen 4 and different trainer classes, all of whom can participate in battle along-side their Pokémon. If you’re working on something, it might be nice to take a peek at that.
I really do like the idea of there being Burst Warriors and Pokémon trainers too! I never read the Burst mangas, but always loved the idea. Something that I’d really like to see is many Pokémon at once, like a horde battle both ways! I never liked the four-move-limit or the six-pokemon-limit; it might be nice to have a whole bunch of Pokémon at once!
What sort of region are you thinking of? One of your own design? I’m kinda interested in playing, even though I don’t know much about Pathfinder (I built a character once, but my buddies fell through and we never played …).