Here's a thing: why exactly are humans the dominant species in the Pokémon world? How come they have the autonomy to capture Pokémon and make them fight? Those Pocket Monsters are crazy powerful, can communicate with each other, start societies why do they put up with all this battling crap? One theory suggests humans are not natives to the Pokémon world. Perhaps that's it. Maybe humans just travelled to whatever world the Pokémon exist in, and made it their own, capturing and enslaving the native species (steady now). It is kind of in human nature (ahem). It would explain why you happen across Pokémon fossils more than human ones. Perhaps there's another reason for that, however. Maybe the humans you play as, interact with and battle against in the games are just a different form of Pokémon. A highly evolved one that's established a hierarchy on which they are at the top. After all, humans can also learn abilities, fight, and heal themselves from injuries in the same way Pokémon can. So why not?
Tom Baker is the Comics Editor at WhatCulture! He's heard all the Doctor Who jokes, but not many about Randall and Hopkirk. He also blogs at http://communibearsilostate.wordpress.com/