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Only because he has "already won". Team Rocket are an established presense, and Giovanni sits comfortably in a position of power.
Magma/Aqua are loonies who attack from a secret base.
Galactic do have their own base, but no real presense or power in the region, they're just a cult.
Ghetsis stayed in the shadows and let everyone believe N was in charge.
Skull were just hooligans, as Yell seem to be, and Lusamine wasn't really leading a villain team.
You're not entirely correct though, because Lysandre exists, and he basically is Giovanni 2, he just snaps at the end.
