Unfortunately, as good and different as an idea that is (and creativity is always smiled upon :] ), it just wouldn't work for the Zelda franchise.
One of the key components of the series is that Link is the hero. He is a hero that is representing all the goodness of Hyrule and the goddesses, he is always mute and selfless and his actions are always to do better for all. It's something that has always been. Never has Link strayed, and he is willing to help even the most suspicious of people (*cough* Cubus Sisters *cough*).
While it'd be interesting to 'choose your own destiny' for Link, the idea just doesn't FIT into the world of Hyrule too well.
At least for me.
I just get the sense that Link is the embodiment of pureness and goodness. I mean, really, he's usually just some basic peasant or civilian, that goes... "You want me to save Hyrule? Okay!

" So... yeah.
But the concept of him turning a little dark, now that I think of it, would be interesting if this entered into the plot somehow. Something is making Link get a rather... twisted view... on things, and say, part of it is that he not only has to save Hyrule, but himself. I'm sure Ganon could warp his mind here and there, and make him perceive things a little slanted.
But... in conclusion. That's a really NEAT idea... But It wouldn't work so well for Zelda.
:]
Nice of you to post a cool idea though, I'm curious as to what other people think. ^__^