*Spoilers*
If you talk to Team Plasma members in N's castle, they'll reveal that they have been using pokemon all this time for their own gain, and they think of pokemon as nothing more than tools (although I think only the higher ranking Team Plasma members knew their true intentions, and most members were just innocent pawns who got manipulated). And Ghetsis himself says he only wants to use pokemon to take over the world. And of course, N is innocent, because he genuinely only wanted to prevent pokemon from being hurt in pokemon battles.
As for whether I agree or not, I'd have to say that I can see their point, but at the same time, there are people who do things other than battling with pokemon. If pokemon were real and I had pokemon, I wouldn't make them battle if they didn't want to, and if they wanted to be free, I'd free them.
Edit: Also, in the anime, when Ash was trying to catch Snivy, she resisted at first, which is why Ash's pokeballs wouldn't work on her, but then she suddenly decided she wanted to go with him (of course she didn't talk, but it was obvious), so the next pokeball suddenly worked.