Does it really matter? Story, character and character development are the important things when it comes to characters in my opinion, all those things can be achieved regardless of what gender the charter.
I don't play the zelda games but it seems pretty pointless and like it will annoy more people that it will please. If I had a character I enjoyed and/or I could relate to I'd be pretty hacked off if they changed their gender for the next game, as who ever they were in the previous titles changing that will integrally change them at least to some degree? for better or worse.
If I had to choose, it would be tomb raider so I could have at least some justification for wearing insanely small shorts, to the offense of all involved.