>>47318698Anime also shows pokemon have the will to disobey, even harm their own trainers. In the very first episode Pikachu refuses several times to return to his ball, shocks Ash and even after being hurt, still retains his defiance.
Pokeballs aren't mind-control devices, as much as a comfy room with food isn't supernaturally bending your will to stay in it.
In the games, Pokemon can and will disobey your commands if they don't respect you enough. The fact that the games don't allow players the agency to truly mistreat their pokemon, doesn't mean the pokemon themselves are meant to lack the ability to revolt.
It's true that the capture system is rather nebulous about it's inner workings, but it seems to me its a simplification/non-stipulation problem rather than outright trying to hide how cruel it might be.