Humans aren't from the Pokémon world. They are from earth. In the year 2056 NASA starts it's most ambitious progam: to take a breeding colony of humans to a new world. After studying a planet relatively nearby (6 light years to be exact) they decide it is the perfect planet to colonize as it is highly likely to contain life, oxygen and water.

They send 10 ships of 500 humans, 5000, the minimal viable population. At 20% the speed of light it takes roughly 40 years to get there. In the time the ship finally arrives new babies are born and have grown up in the ship and taught all the knowledge of the human race. The planet of course is the Pokémon World where life and evolution works much differently than on our world...