RE: What would happen if Pokemon were the dominant species in the world.
Like Atadiusti, I too don't think that humans are the dominant species, at least for now since they still rely heavily on Pokémon. I don't know if this is the way the creators wanted it to be by showing us a more friendly world without machines, industrialization and lots of pollution.
When it comes to Pokémon, I think they're dominant as a whole since their numbers may surpass ours but if there was to be a dominant Pokémon...Arceus! Sorry, I had to bring this one, because it's the creation Pokémon, not only that but Palkia, Dialga and Giratina are like gods, feared and, in some ways, worshipped (that church like building in Hearthome is some proof to that). What else there's to say after knowing that there's a creation entity that happens to be a Pokémon? Sure, it's stupid when Arceus can be captured and even befriends humans like it were some pet, but it's still there.
I don't know why Arceus created humans but having the creator of the universe being a Pokémon means something.
Also, don't forget Pokémon like Clefairy and Deoxys, Pokémon from space, so "Pokémon" don't exist only on PkEarth but also somewhere in space, in the moon, places where humans have yet to go so another clue to think that Pokémon are dominant in numbers, they just have yet to remeber that they can slave and destroy humans almost in the blink of an eye.
....
*goes rally and chat with some Pokémon, namely the Musketeer trio, a couple of legendaries and try to create a new world order*...