Where to start?
Blastoise, Salamance, Metagross and others would be used in wars as powerful weapons (Metagross is missle-proof, good luck trying to take that down, soldier.), and would probablly be abused to the point of endangerment/distrust of humans.
Mewtwo, Shadow Pokemon, Perhaps some Porygon-Z and other Man-mades, Most Darkrai and countless others would try to destroy humanity for various reasons, from being created and used as nothing more but mere tools, to wanting to shape the world in their image, to sadistic just wanting to see the world burn.
Pokes like Pikachu, Cleffairy, and Rattata would be kept as pets, and would be the main ones used for the "primairy" purposes of battling, contests, ect.
Some of the smarter pokémon (Gallade/Gardevoir and kin, Alakazam, and Slowking) could possibly start civilizations of their own, if they're not hunted down by man.
Legendaries like the Weather Trio and the Legendary Birds would be displeased with humanity, and lock themselves away.
And still a few, like Mr. Mime, are completely unaccounted for... What did that sound come fro- *Thwap!*
Anyways, our world is completely unready for pokémon, and although it might sound cool on paper, the results would be chaotic at best and destructive at worst.