Like any RPG? Nah. C'mon, in most RPGs the characters are brought together by the story. Even the occasional antagonist who is fought and then allied with has a whole discussion where they are convinced of the merits of the protagonists. I could grant that in the Pokémon anime fairly often the creatures are convinced or decide to come along willingly, but in the games that hardly ever happens.

How do you reconcile the idea that the creatures want to come along with the active resistence of fighting them and having them break your pokéballs repeatedly?

Of course if you take the story by its word they'll say that trainers are good and friendly and only these criminal teams really are evil. And for fun I indulge that fantasy while I'm playing it, that these are martial artists pets that just love fighting so much and that pokéballs must be super comfy inside. But if you take a moment to compare what is happening you'll see that it isn't that different from what Palworld is doing.