I know this is a bit of topic but I was wondering... Why don't the Pokemon just- Y'know... Rise up and kill the Humans? There's no reason they couldn't, Humans don't have any powers, Pokemon do. And a lot of Pokemon are smarter than Humans too. There's never any explanation in the games or manga as to why Pokemon listen to Humans, if I were a Pokemon I sure as hell wouldn't... "You want to put me in a tiny round capsule? How about I rip your face off?"
Any way, I'm going to tie that into the topic at hand. My theory is, as some have suggested, is that Humans evolved from Pokemon. When they evolved they lost all of their powers but gained an ability or move (like a Pokemon ability or move) to command other Pokemon. Eventually over the course of hundreds/thousands/tens of thousands of years they stopped considering and calling themselves Pokemon, but instead thought of themselves as higher beings, Humans.
That's the only explanation that makes sense to me, but nothing like that is ever brought up... I still love Pokemon, but every time I send out my Dragonite to fight for me, I still wonder why he doesn't just turn around and hyper beam me in the face... Seriously, what's there to stop him?