What aspects of the franchise do you see as Unacceptable that, with some logic and realism, could be deemed as acceptable?
To kick things off, throughout the games, series and movies the scientists have been idiots. All of them. Regardless of how advanced their technology is they have a single, burning, quite possibly very simple question.
What are your opinions of what have become the only animal species to inhabit the world? Where did they come from? How do Pokeballs effect them? Why do they fight for people? Why do people make them fight?
Personally, the only acceptable answer I have for why Pokemon fight for humans is because they NEED to fight. Wether it's to achieve a goal or just their nature, Pokemon need to fight. At some point in time Humans became moderators, someone to hold Pokemon back from wiping each other out.
As for Pokeballs, I find it unacceptable that a wild animal you beat down will so readily become your friend, something Ash has done at the beginning of every season. Whatever their past intentions were Pokeballs are now used to brainwash the Pokemon within. During the MewTwo special, when MewTwo crushed the hunters Pokeballs (*snicker*) the Pokemon who had been linked to those Pokeballs walked away aimlessly, like they completely forgot about the fight. Wether a Pokemon chooses to get put into a Pokeball or is forcefully taken from the wild they are all subject to brain washing. Perhaps they still have some degree of free will depending on how they feel about their trainer, but their free will is altered to better suit their trainer.