You can't really question too much about the origins of humans in the pokemon universe, in any of the games. I mean, it's not like humans would just pop out of the ground, they'd have to evovle from something, but there's no monkeys/apes/non-pokemon animals for them to have evolved from. You can't relly say they could have evolved from Ape/monkey-like pokemon because none of the powers pokemon have appear in humans.

Clearly the answer is that humans are actually alien invaders that have been on the planet so long they forgot their origins.