Are humans technically their own Pokemon species in the Pokemon world? Maybe they just don't classify themselves as Pokemon the same way we don't classify ourselves as animals, even though we technically are. Perhaps humans were the dominant species of the Pokemon world and had an advance intelligence far greater than other Pokemon, that they were able to control them? There are a lot of humanoid Pokemon and humans could be closely related to them. Pokemon weren't even referred to as Pokemon (Pocket Monsters) until Pokeballs were invented. There's even a book in the Canalave Library that mentions there was a time period where humans and Pokemon were considered to be one and the same.