Im questioning the importance of Link being the main hero in the first place. Of course Link is a boy, thats who he always was. If a female role was being added to the series she should be a separate character from the Link we all know and love.
For an example of how this works wonderfully, The Witcher 3 you will mainly play as Geralt, but have the option also to play Ciri.
It does seem dumb though to add a female character just for the sake of being a female. That's something Dragon Age does very obviously.