The problem is that we haven't actually seen a proper Ganon in any of the 3D Zelda games yet. OoT Ganon has a really great look, but he is burdened by a really simplistic fighting style. Classic Ganon has an insane moveset: teleportation, invisibility, a wide range of magical attacks, an awesome trident that can move of its own accord, and the ability to create doppelgangers. You see Twlight Princess Ganondorf show off a fraction of this when he summons a squadron of mounted Phantom Ganons to attack with during the mounted segment of his boss fight, but that is about it.
If you were to take the appearance of Ganon from OoT, give him the moveset of ALttP Ganon or ALBW Yuga-Ganon, and let him dominate the story from the beginning, I think that more people would be fans of classic Ganon.