Ganondorf is only one incarnation of Ganon who himself is a incarnation of the final boss in SS (for spoiler sake I won't name him). The's no reason for Ganondorf to be around tbh, great villain but the recent villains in Yuga, Zant and Ghirahim have brought a different type of antagonistic approach rather then the dark brooding type to the series with one being crazed on a level only the Joker can comprehend another being theatrical and narcissistic and the final one being artistic (won't spoil what happens in ALBW).