Ummm, but isn't Link supposed to be the same character all the time? Unless you include some gender bender magic, there's no way to make Link female while maintaining him still being the same character.
I mean, they didn't go and make Carth a woman between KOTOR1 and KOTOR2? In KOTOR2 they even let you decide what gender Revan was according to what you played in 1, which was neat and I'd be quite cross if I finished 1 with a female Revan and then in 2, all the talk would be about "him". Even if Revan was canonically male.
That said, I am not opposed to a female Link. As long as it's justified and explained how come he's suddenly a "she".