I'd prefer to be a trainer simply because being a trainer implies being a human. I wouldn't really love to get captured and live inside a Pokéball and only come out to battle and stuff. Freedom is something I really care about and I think being a trainer's Pokémon would take that away. Sure, I would develop a connection to my trainer and probably be happy, but you do get what I mean right?
Also, even though I could be a wild Pokémon that never gets captured, I don't know how different Pokémon's brains are from humans and how evolved as a species they are to have their own thoughts. I don't know if they can dream, if they can think or develop ideas, if they solve problems, etc. I don't feel like they can read or create stuff, just like we humans do! Sure, I would LOVE to be able to fly or to explore the seas, but, being a human and knowing our capacities, I would not like to become a Pokémon and only live based on my survival instincts.
It's a complicated question :/