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Something I always remembered about d/p/pt is that Rowan always put an enthesis on what would happen to the protag and Barry if they were to go in the tall grass without pokemon. Like they would get seriously injured just by a encountering a level 3 Starly.
Even weak Pokemon are pretty damn strong in comparison to humans. If a Pokemon dislikes battling and hates their trainer, they could very well retaliate against them. Easily. They also straight up refuse to follow your commands if they don't respect you, and in the anime they can refuse to get in and out of their pokeballs. Friendship is also a mechanic used to evolve and strengthen them. They're generally smarter and stronger than the average irl animal used in fighting.
If a pokemon is letting their trainer abuse them, its most likely because they love the trainer too much to want to fight back. Basically, they're being taken advantage of. Or they're super weak and stupid and the trainer has a weapon or is in numbers.
Idk, this is a retarded explanation but its a kids game and most kids don't think about this.