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But there are Pokemon owned by abusive trainers who are unhappy.
Every single region has gigantic criminal organisations that do this, the problem is utterly universal. Not to mention that there are likely many abusive people out there who treat their Pokemon badly naturally, like abusive pet owners, who have nothing to do with organised crime. And also, remember this; in the logic of the game the player character is often suggested to be some kind of especially caring or intuitively "in-tune" trainer who gets the best out of their Pokemon. This is used to explain how you are such an effective trainer, as in Oak's speech when you beat the league in Gen 1. This could suggest that the PC is actually the EXCEPTION in their level of friendship with their Pokemon, and most people are not as caring as you.
All that would be bad enough, but we're not even really talking about pets here. Pokemon can apparantly communicate with some form of language, suggesting they have person-level intelligence, with some of them explicitly being said to be more intelligent than humans. N's philosophy is correct. The fact that there are some good Pokemon trainers does not address the central issue of whether or not OWNING another person is morally acceptable. There were nice, kind slave owners too, but they do not counterbalance the abusive ones, slavery was wrong in either case because it was the treatment of another person as property. I am glad that BW2 didn't cop-out and have N do a 180, from the dialogue he still believes that one day we will be able to be partners with Pokemon "without Pokeballs."
