Theory #1: The Fairy Queen from Wind waker is the reincarnation of Fi of Skyward sword
In the end of The legend of Zelda Skyward sword Fi told Link she is going to enter on an endless dream on the sword, lets say she is the sword spirit, so years passed and we get to Wind waker, on wind waker we find The fairy queen after pulling the master sword, at this point the sword had lost his power, and we need to find the sages of earth and wind to recover it, so at the point Link pulled the sword from the pedestal, The original Fi died, Reincarnating on the Fairy Queen,
you can also hear Fi´s Voice on the music of the fairy queen meeting.
[video=youtube;Y_hdTMM9qaU]
http://www.youtube.com/watch?v=Y_hdTMM9qaU[/video]