I just came up with an idea/story setup that would make this idea make sense.
The game takes place a century or two after the last Hero whopped Ganondorf's bum and got him sealed up in the Dark World/Void/wherever he gets customarily sent to. Ganondorf has just broken free, having used most of his power to do so (Triforce of Power aside). Ganondorf is still big, bad and powerful, but not as powerful as he used to be. He can command a few minions (dark creatures that come to him from out of the wilds), but he doesn't have quite the command over, nor the ability to conjure the greater beasts (at the beginning of the game).
Going through the temples himself is how he gains his power. He can only get his full power back by killiing the Sages that guard the temples and appropriating their power for his own. Now, the Sages in Hyrule at this time are *especially* strong... as in, Ganondorf cannot trust a mere dragon, or sandworm, or evil acid spitting plant or whatever to dispatch them. Only the King of Evil can match their strength.
The Sages start out as lesser to the greater as the game goes on. Say, the little Forest Sage might be the first. Her power is beyond mortal ken, but she is the least among the Sages. I imagine that the Sages don't *just* have a humanoid/standard race of Hyrule form, but have an alternate, uber-powered form you'd have to fight. For example, the Forest Sage might become something representing her element - such as a great battle-deer or a freaky Ent-like creature after Ganondorf first engages her. Upon defeating her, Ganondorf gains her power. (Perhaps represented by a little cauldron-symbol for magic much like Link gets heart containers to represent life/strength/stamina). He now has the power to go to the Fire Temple, corrupt it, and kill the Fire Sage.... and so on. He must murder all the Sages (save perhaps one - if Zelda is a Sage in this) in order to gain ultimate conquest. He gains the variouus elements/strength from all the Sages, THEN he can go for the Triforce, search for Zelda and fight Link.
And since this is a Ganondorf game, there should be an option of him succeeding, as in, in the Timeline continutiy, this game becomes the game where people in future games speak of the "fallen Hero and the extended time of Darkness."