Zelda is all about playing as Link, playing the technically inferior warrior, that slowly gains strenght, but really excels in bravery.
Thats what OOT was all about and what I loved about it so much, Ganon got the Triforce part of Power and Wisdom or something, but Link the Courage part. His courage and determination and pure heart are his real skills, and those turn into his battling skills. But technically, Ganon or Ganondorf for that matter, is always more powerful.
Also I am convinced it wouldnt fit the Zelda series if Ganon/dorf and Link team up, its just wrong. As someone said before, Ganondorf is THE evil, when playing OOT (I was younger, but still) his character really frightened me, this insane power and incredible evil, really intimidating.