Ganon has only been in 6 Zelda games by my count. LoZ, ALttP, Ocarina, TWW, TP, and FSA. Seven, if you want to count the linked game in Oracles. That's seven out of fifteen, less than half. If anything, Ganon isn't used enough. He's the principal bad guy in the series and shouldn't be left out just because "Huurrr duuurrr overused." It's like Mario without Bowser. It's like Castlevania without Dracula. Ganon is as much a huge part of the series as Link or Zelda.
Nintendo showed us that, if they wanted to, then can actual make Ganon interesting, ala The Wind Waker. In games where he just sort of shows up (FSA, Oracles, TP) it's understandable he has no real personality. Even still, his pen-ultimate speech in TP was awesome, right before you fight Puppet Zelda. TWW showed us a Ganon who has been defeated and had time to reflect. TP showed us a Ganon who has never lost, and survived death itself. Meanwhile Ocarina showed us the "younger" Ganon who was confident in his abilities, and thus, he underestimated Link. In LoZ, Ganon was just this evil looming presence, and for a game that simplistic, it's all he had to be.
So long as they give Ganon a more fleshed out personality I'd love to see him return time and time again. Let's face it, today people demand compelling plots, and therefore they want compelling villains. Yes, he was out of left field in TP, and Zant received the character development being seen as the "final boss" for much of the game. But I feel that if Ganon is shown to us early on and we know he is a clear and present danger, than Nintendo could really make him interesting.