Pokemon makes no sense at all. I mean there's no point in this, but if we're going to take it apart we might as well do it well.
Legendary pokemon work just as efficiently without a trainer. There are also cases where Pokemon become great fighters by themselves due to the dangerous, or harsh, environment.
The pokeball idea is ridiculous, but understandable since it's an anime. They still ride bikes when they have amazingly advanced technology. They could be riding hover bikes or something cool.
When a person is trying to steal a pokemon, they rarely target the trainer. If the thief took out the trainer then they could just grab the pokeballs and leave.
Only Meowth (and Mewto.. maybe more) was able to talk, but somehow every pokemon can understand the human language. How can a wild pokemon understand human language, yet not speak it?
There is almost no possible way to tell between a male and female pokemon.
The criminals in Pokemon have to be complete morons, since it only takes one very strong pokemon to wipe out a town. By taking out all the trainers the vilians would be free to do whatever they want.
Pokemon are able to such destructive things, but whenever a human is hit by an attack they don't even get hurt (flying in the air and being pure black doesn't count).
Pokemon only faint when they should actually die (yes I understand it's a kid show I'm just going throw the problems with it).
A trainer seems absolutely useless to a pokemon. Pokemon have been known to band to together and work perfectly fine, by themselves, as seen by the Squirtle Squad. A pokemon can get it's own food and has more freedom in the wild. By capturing a pokemon, you do nothing for it.
Pokemon have no desire to become stronger (unless like Mewto which proves my point anyway), so by capturing it your just forcing it your own will.
End conclusion: Pokemon is a show about slavery.