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They tried to address the moral conundrum of Pokemon Battles in BW, but sort of hand-waved the debate. It's a front for Team Plasma, and you aren't really supposed to think about the issue.
I think DP weirdly paints a more nuanced picture by having your Pokemon "talk" about their worldview. They are very intelligent. Pokemon with lower friendship will be uneasy about humans and Pokemon captures until they warm up to you. Pokemon with high friendship talk about reaching their full potential, evolution, being well fed, taken care of, etc. Some Pokemon stay out of sight because they hate the whole setup of trainers. I like the range of thoughts that you get.
