In the games, especially since Giovanni vanished from existence after RBY/FRLG and has no context aside from the anime and games, Cyrus has the victory for "best villain" as his plot is the only really villainous thing in any game; he's trying to DESTROY THE UNIVERSE AND REBUILD A NEW ONE HE RULES... that's textbook villainy at its best. While his character was poorly developed (the most developed were definitely the two teams in RSE and the two Collo game villains), his plan was actually villainous and rather clear-cut. The two teams just were fanatics for whatever cause they followed which isn't inherently evil, Team Rocket (within the game context) were just petty thieves and mafioso looking to corner the economy and steal trainer's Pokemon (and when the two could be intertwined, awesome to the max). It isn't without the context of the anime or manga do we get a real context for the depth of Giovanni's scheming for control, though really that just makes him your stereotypical "Mafia-run-state leader" in aspiration (a more maniacal Big Daddy for any Gungrave fans). In XD, the various snagging and shadow organizations were just Fail!Team Rocket with OMGTHEPOWEROFSCIENCE!1 If anything, they were more annoying douchebags than villainous ("Oh man, you're taking other people's pokemon and... making them... not be nice... but they still follow orders and do Pokemon battle things. ... ... ... oh.")