I think it would be cool for a DS game... It wouldn't be popular but it could become a cult hit...

I can totally imagine Ganondorf being the "hero" in an alternate universe...

They could make a new interpretation of Ganondorf, this version would be the type of person who does whatever he has to do for the survival of his people, rather than a power-hungry tyrant. ... he would still use dark magic and some less-than-noble tactics, but in the end it would be for a good cause...

In this game, the king of Hyrule stole a very valuable item from the Gerudos that is crucial to their way of life, and as the king and protector of the Gerudos, Ganondorf sets off to retrieve it.

In the end he faces off against Link, who is not necessarily evil, but was sent by the king to protect and defend Hyrule... after losing the battle, Link's life is is spared, and the king exposed and dethroned. The new king then allows Ganondorf access to the triforce, where he touches it and wishes for his land to have peace and live a prosperous life so that they no longer have to make a living by being thieves...

There would be a couple of kinks to work out, but in the end it actually could become a great game.