Ganon isn't overused.
It's just that he's been used in the wrong way in recent games.
But really, even then, the naysayers don't have much of an argument. For
FSA, yes, he was sort of tacked on. For Twilight Princess, hell no. The entire game was building up for him to appear. If you played
OoT, you'd know that Ganondorf wouldn't have simply been killed on the Child Timeline.
What most people should actually complain about is how much screentime Ganon gets. For the games of LttP and prior, Ganon appears at the end, as the "mastermind." In
OoT and WW, Ganondorf is visible at certain points throughout the entire game, which is perfect, and I'm certain what most people want.
For Ganon to be used properly and be warmly received, there can't be another villain involved, or at least, he needs to be involved alongside a villain in all the games events.