>>48904971Pokemon villains are at their best when they're just some assholes or relatively petty criminals. This is why Team Rocket has lasted so long as far as popularity goes, or why Team Skull is so beloved by the fanbase. The closest you can really get to an end of the world plotline without having it be ridiculous and stupid is like, Team Plasma and Ghetsis.
That said, evil corporations are relatively underexplored in the setting, and would strike a nice balance between "pokemon thieves" and "building a gun to blow up the planet", maybe have some personal investment in it for the player, like they're trying to shut down the rec center or some shit