And Mewtwo most likely take over by himself, he is the most powerful Pokemon (Don't bother, Shadow)
And smarter or not, a trainer is there to make a Pokemon better than what it already is. The kind of help a trainer gives can't be achieved alone. In a battle wild Pokemon rely on pure instinct no matter how high their IQ, but with a trainer there to guid it it listens to his tactical commands instead of its insticnt. Not only is there the concept of the Pokemon getting better, but moral support aswell. A bond between trainer and Pokemon. A Pokemon listens to its trainer well when it full trusts him. A trainer will do his best to keep the Pokemon from getting injured in a battle. Which brings up another reason. In the wild Pokemon that loose a fight either crawl away injured or just die. With a trainer Pokemon are almost certainly guarenteed restoration after a fight. They get to retreat to the saftey of the Pokeball and healed at the nearest PokeCenter where their wounds are treated and they get feed.
I could go on and on about it but I'm sleepy.
But I hope that clears it up.