Now to play the devil's advocate.
I was thinking about the 12th movie Arceus and the Jewel of Life lately, and it reminded me of this thread and the question of pokemon being enslaved, particuarly the theory that the pokeball brainwashes the pokemon.
Its not a far stretch. In the aforementioned movie we saw Pokemon visibly unhappy in a time that proceeded the invention of the pokeball. It is system we would immediately recognize as slavery, where pokemon were threatened and chained.
Maybe the system of exploitation never really ended, but just became more sophisticated and subtle with the advancement of technology. Just because you break someone's bones does not mean you succeed in breaking their spirit. There were pokemon like the villain's Brozong who ultimately stopped complying even at the risk of feeling their trainer's wrath. Maybe what we learned as humans is to hold a pokemon's soul in captivity through the pokeball, not just their bodies by prodding them with a rod. Though is gen 1 we did see some trainers still carrying the whip.
A pokeball is not a Pokemon's natural habitat. Its a tool used to confine them, I think everyone would at least allow this much. When we encounter a pokemon we want in the wild we generally take them by force, it's not up to them whether they want to come with us or not. While there are some situations where Pokemon seek out trainers and express interest in joining their team, this is rare. Pokemon almost invariably try to flee, fight back and break out of their pokeballs.
There is no question of a Pokemon working with a trainer of their own free will at this stage. Yet as soon as pokemon are captured they come out calm and obey their trainer's every wish, even though they may have literally gone into the pokeballs kicking and screaming. What could have happened in such a short time to change their mind?
Before pokemon even have the chance to get to know you, train a single level or take one footstep out of the pc Pokemon are yours to command. There are Pokemon of all different species, sizes, genders and natures, yet the overwhelming majority of them as soon as they are captured are set to a default friendship value of 70. It does seem like something is being done to them once they are trapped in the pokeball to change them.
It's not as though we have not seen a pokeball change a Pokemon before such as the case with the dark ball in the Celebi movie. It gives you something to think about...
If a pokeball is potentially brainwashing the Pokemon then it undermines the arguement that Pokemon are happy with their trainers because they have been compromised, and can't realistically be expected to evaluate the situation in the same way that you or I would. It would be like drugging a person, then taking their money from them or molesting them, and saying that they look like are happy eith you doing these things to them. To say the least it may not be an agreement that this person would enter into if you had not impaired their judgement.
"Pokémon are nature. Poke balls are civilization. Humans who are used to civilization don't relinquish it easily. Of course, both nature and civilization are important. But what will happen to a world taken over by Team Plasma? People will be forced to throw out Poké Balls--a product of civilization. I want to know what that looks like! And I want to enjoy it!" - Zinzolin of the Seven Sages