Ganondorf is the King of Evil, nobody can match him except the Hero. There really is nobody who can be eviler then him. Vaati especially has been proven to be oneof Ganondorfs tools.
Also, Ganondorf isn't overused yet. His character still has a long way to go regarding background, motives and a multitude of other factors. He can be in the next Zelda, but obviously he has to be there as much as Zant was in
TP.
And for those who think Miyamoto cares nothing for storyline, you are clearly wrong. Obviously he knows storylines are important, but he prioritises gameplay over story.