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Let me preface that I'm aware how silly it is to overthink a children's franchise. So with that out of the way are pokemon battles comparable to cock fighting?
One of the excuses against this is that according to some pokemon like fighting naturally and seek out trainers in the wild. The problem I see with this is that there are dex entries which specifically point out that some pokemon species don't like fighting and there are wild pokemon that run away from you. In fact according to Lapras pokedex entry they are gentle creatures who dislike fighting and people take advantage of this to have an easier time capturing them. And the existence of pokeballs and the master ball kinda go against this since it's clear a pokemon struggles not to get caught and a master ball makes it so that they can't resist. If they really want to join a trainer there's no reason to forcibly capture them since they can yield if beaten enough imo. And of course there's the implications that come with it such as a trainer breaking up communities, those pokemon probably had a family, and acting as an invader. And of course leaving a tainted pokemon in the wild isnt the best idea.
Second pokemon do get abused and abandoned. People again point out that Pokemon can run away if they're not pleased with their situation. But this ignores what run away entails. Pokemon have no agency of their own, they depend on their trainers for everything and their trainers own everything about them, from the fruits of their labor to their children. Pokemon do no exist as individuals legally speaking but more akin to property. Second it's very likely a captured pokemon is fairly far from their home. And third a domesticated pokemon would be forced to like as a stray seeing as they don't have any experience living in the wild. There's also intimidation and complacency from the other pokemon.
In short it looks pretty fucked up if we go overthink a children's franchise about capturing monsters.