I don't mind it. Several anime episodes have shown characters that have learned that some of their caught pokemon enjoy becoming stronger with training they might not obtainer without a master and enjoy companionship.
I think it did pretty good. It could've gone deeper, sure, but I think the point of it was that the player could decide how they felt. Also, I liked that there was no definitive answer. There were plenty of arguments for Pokemon being with trainers but the people against it had some pretty good arguments to: most Pokemon live longer than humans so it'd be cruel to make them watch you die while they live on, sometimes humans overwork their Pokemon, and it could be considered cruel to send a weaker Pokemon into battle.
Considering that they never really gave us a solid answer about the morality of capturing Pokemon, I'd say no. They had the Plasma-dan (Team Plasma) spout their beliefs about how Pokemon needed to be liberated, but they were lying the whole time, with the exception of N and a few grunts.
I loved how Game Freak tried to tackle that lesson in these games because it was something I always wondered about. Pokemon battles always seemed cruel to me so having Team Plasma advocate against catching Pokemon was a cool way of diving into that even if they were working towards their own evil plans.