If they just made link female, you can bet you would have a load of people ruffled because "its just a pallet swap its no different", and that's excluding the people that would point out that they were messing with the formula for the sake of messing.
Basically there is a good chance that you could annoy 2 groups of people by doing it so i doubt they will.
Also people are saying why does it have to be a man, well the lore does kinda state this bit as its for the same reason Zelda has to be a women (something that people in this thread seems to be accept).
Zelda is the reincarnation of the goddess hylia, and link is the reincarnation of the legendary hero that hylia took pity upon, hylia gave up her godly powers to be with him throughout the ages because of his sacrifice and service. This is in the manga that came with the Hyrule Historia which was confirmed cannon i believe, and also kinda reinforced at the end of skyward sword (not that i've seen it, only game i've not finished outside of the DS ones)
What would be a better wish for the game would be for Zelda to take a more active role ,help out, join you , rather than just be kidnapped as normal. As that way there is a better female role model, using an already established character and you don't have to rip up established cannon/ruffle feathers to do it.