I think it could've gone either way with Team Rocket. In Hoenn especially I didn't particularly care for Aqua and Magma, yet with Rocket it would've gotten stale pretty quickly. Same goes for Sinnoh.
The problem I think is if you're gonna keep making new evil groups you have to keep coming up with innovative goals for those groups, and if you end up with "taking over" you might as well just put Rocket in the game. As for Pokemon, I feel like there are those Pokemon like Zubat and the random others that are just grunt Pokemon. ;P