very interesting, I actually read the whole thing. As fan fictions go this is one of the nicest I have read, I actually felt depressed at the start for Link missing his love :P .
As far as a sequal to TP goes it is fairly solid, apart from the fact that Link Speaks, and that Link has never had a real love interest. It is a very mature view on the world of Hyrule, and one that I would welcome whole heartedly. The possible dual character setup could be a breath of fresh air into the series, it is also a dark view on the world (even more so than TP) which in my eyes is a good thing. We all know it won't happen, Nintendo must receive thousands of fan fictions for their various franchises, but as far as speculation goes I would like to see a sequal to TP, and something in this vien wouldn't go amiss at all. But alas when Nintendo make their Zelda games, Link is as blank a canvas as possible, meaning any character relationships are all fan made. Were Midna and Link in love? That is up to the player and to an extent is the base line to Zelda games, the player decides who and what is going on bar the main storyline. Therefor fan fictions are born based on hints left within the games. Ipersonally would like to see a more personal Zelda experience where I am told the story, instead of making the story ala FF. Your fan fiction reflects this wish and harks to a time of story telling not story making. We know it won't happen, but let's hope your ideas and many like yours are taken on board and a sequal to TP is released with more fleshed out characters.
All in all a very good effort. One of the best fan fictions I have read regarding the Zelda franchise, and a good read regardless of said franchise.