Lets be honest, Link would have been so much better as a girl, plus besides Samus there isn't many female protagonists in games. Since Nintendo is Japanese they could probably get away with the underlying lesbianism between Link and Zelda anyway.

I think it would be nice to just have a break from a male link, Ive been working on a formula for a co-op zelda title (i feel the Wii U is a great platform to do so on, what with the screens on individual controllers) I feel a female protagonist would be incredible in a zelda game, and a great chatty counterpoint to the silent male version, while also doubling as a navi-esq guide in tight spots.
Her weapon could be different, her aquired items could be unique but complementary to the male counterpart, and boss battles would be way more dynamic requiring teamwork. rag along AI builds could take over the idle character, as well as being switched out at will to prevent the snags of tandem fights need for precision action. Ie Hook shot a large boss to the ground and have the more nimble female Link to run up the length of the back or neck to strike a weak spot.

Also this presents amazing potential for puzzle solving what with character specific items, and an amazing resaon to use the screen controllers to seperate the two characters amongst the overworld (using the television as an overhead map) While maintaining tight controls and adding a new and exciting reason to sit down with a buddy on your couch.

A man can dream....

I like your ideas, I don't see why this couldn't be introduced into a different series though. It would be kind of awesome to play a game that requires that much teamwork where one of you plays as a heavy, strong fighter type character whilst the other plays as a more nimble rogue. Could make for a very interesting title.

I agree! Either way it would be nice to experiment

No protaganist, but a majority of the main characters in Zelda, or at least from what I recall, end up being female. Hell, all but one of the sages in Ocarina are female.

That's left. (second person I've said that to today ...)