Having read through this thread and its replies I'm most favorable towards Ganondorf and another villain working towards the same evil end. After Ganondorf realizes his plans have been thwarted, however, he feigns the role of a noble hero and teams up with Link and Zelda. Once the opposing antagonist has been defeated, Ganondorf reverts to his evil ways once more, turning his back on the other two Triforce wielders.
This nuance was thoroughly explored previously in a different Nintendo franchise-Pokemon. In the fifth Generation games, the trainer isn't only endeavoring to subvert Team Plasma but gain further insight into a mysterious figure called "N" bent on Pokemon liberation. N's good intentions, however, only cause more mayhem about the Unova region. The Zelda fanbase has incessantly complained about stale plots; this is the perfect opportunity for Miyamoto and crew to spice things up. Throw in some other recent ideas circulating around World of Zelda including optional companions and you've got a truly original title.