Team Plasma has the distinction of being one of the first teams to canonically use a legitimate argument, even if it is fueled by the emotive side of the brain, as their primary motive. (Aqua/Magma had their merits, but were well-intentioned extremists that'd be classified as eco-terrorists.)
While some sources claim that Pokemon can only find happiness in battle, and that trainers help them achieve their highest potential, clearly there are other examples of pokemon being just as varied and diverse in their wants as humankind - some pursue stardom in contests and like challenges, others are into the care of young (examples in many games of pokemon looking after human children), simple companionship, and, yes, some do like to battle.
Due to the language gap (sans psychic pokemon for translation), and technology that allowed human superiority in the barest sense, it is entirely possible that things can be taken too far. IRL, humans are the greatest pursuit predator in existence, and are used as an example of that thing that just keeps going and going, and showing up when their prey through they were safe. The same could be said of collectors in world. There would be ethical issues involved with having a single person completing a Pokedex in the realities of the Pokemon world, because unless you were creating an entire ecosystem and reserve, there would be no way to care for them and see them comfortable/tended/have all of their needs met. There would also be the potentials of battles taken too far, and B/W gives us so far the most adult lens in the entire series without quite pulling back that curtain.
I personally love that B/W forces the player to really think about things, and where they sit in the scheme of things. Right and wrong are, oftentimes, culturally dictated. How does it look when someone from another culture learns how the subject works? How does it function when judged by the values of itself, or another culture's value?
Simply put, I feel like many pokemon see their relationship with humans as symbiotic - they both stand to benefit from it. But I doubt that every single one has the same perspective, and I imagine that the pedestal that humankind is put on in the Pokemon world may very well grate against some and cause resentment.
