Considering since the very beginning him, along Zelda and Link, were the main focus of the game, I don't see why he should leave; his last appearence merely disappointed but that doesn't mean it should be left on this. Like it has been said, if he was to reappear with his TWW personality, it could be a benefit for his character.

Also, there's many "new villains", they merely don't feature the most often in the Consoles episodes the most often, but in its sequel or others episodes. It's also since the beginning that nearly all console episodes are made with Ganondorf as the main villain, except Majora Mask I think.

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