I belive there is already a thread on this, but i'm not entirely sure.
Anyway-
I belive that if a villain is constantly reused, as Ganondorf is, they become less popular with experienced or older players. One can even guess what is going to happen, as if the villain is repeated, story elements are normally repeated too.
If the series is kept fresh with constant new villains, it adds more flare and appeal to new players and older players alike. It also keeps interest levels high, and eagerness to buy the next game increases as the player (if they're determined enough) would like to see the next villain without spoiling it for themselves online. (at least in my personal experience)
As a final statement, i'd like to say (and I think I may receive some negative comments about this) that I belive Ganondorf is becoming a worn out villain. Yes, he is the villain that made the series, but still, if he is constantly reused and re-used over and over again, he'll become a boring add on to a dying series of repetitiveness.
The formula needs to be kept fresh with new villains and spiced up storylines. That's what keeps a series interesting and appealing.