There’s other settings where people are literally getting mind-controlled to work for an evil overlord, with a scrappy young group of freedom fighters running disruption campaigns against them. But the setting needs to be reworked entirely from the ground up.
I think such a setting could occur in Pokemon, but it just hasn’t been written yet. More importantly though, Pokemon is aimed at a younger demographic who wouldn’t appreciate such a story. And indeed: Sonic SatAM’s problem was the lack of toy sales. A lot of these cartoons are toy-commercials after all, as that’s where the real source of funding is. If the comic/anime/cartoon fails to sell toys, the whole system falls apart.
These slightly darker and more complex stories about freedom fighters (Sonic SatAM), or conspiracies (Young Justice) tend to lead to superior shows… but inferior toy sales. So everyone reverts to a happier storyline a few years later and My Little Pony suddenly shoots up to #1 (no offense to the Bronies out there, but yall spent money on those toys and it supported that universe…)
EDIT: I should probably note that Team Rocket in the Pokemon Special manga is a secret organization controlling large swaths of the world. In fact, the above fight is Koga vs Blue. Yes, Gym Leader Koga was trying to kill two kids, because Gym Leader Koga (future Elite 4 member) is an elite agent of Team Rocket.
That’s not “capture” or any soft words here. Its literally kill. Koga even resurrected a zombie Psyduck as part of this arc.
In the Pokemon Special Manga, Team Rocket is a serious world threat with deadly consequences. I mean, imagine what a criminal ring could do with legendary creatures, especially when said criminal ring has already infiltrated multiple members of upper-class society (Ie: Gym Leaders and Elite 4).