I think it would be neat to have a game from Ganondorf's perspective. What if it was like an anti-Link game, set during Link's absence of 7 years in OoT.
Instead of healing the land with each action, such as purging monsters from the forest, freeing the Gorons, filling the lake, etc, Ganondorf would do things that harm the land. He would become bonded to land's devastation similar to how Link bonded to the land's restoration. Hyrule could get visibly, musically, and atmospherically worse as you progress.
Ganondorf could also work to capture the sages. They would be the final bosses of the temples, and you would seal their power away at the end of each battle, followed by the respective evils occuring to the land.
Ganondorf could really add lore to the game. I mean it would be great to see how the battle went on, how everyone reacted, and what Sheik was doing at this time. This idea has more great possiblities the more you think about it. It could be an interesting twist on a classic game.