I played after I saw a little spoiler(and I played white2 first), so I knew he was bad, but I believed it's worth think about it. But I heard a kind of "Doesn't Pokemon flee from trainer whenever don't want" question in a city(maybe Opelucid), I thought it makes sense too.
Let's think Pokemons are like pets, e.g. dog or cat. Should we free the dogs or cats for them? No, that's quite risky for them. But many train dogs for humans. It's not bad... Well, through battle, Pokemons can hurt.. but in the Pokemon world, it's incredibly easy to heal than real world after fighting, and it's all free. So.. I'm confused. I don't know exactly way to live in the Pokemon world. But according to N, Pokemons are happy on the battle, so maybe I should believe it. It's really complicated question. Phew. Whatever, it's not the real world.
Another subject is full potential without human. The answer is definitely nope. That's why education exists.