Mixed Review...
First of all, I'll ignore the whole Zelda aspect of it and focus on the execution.
You did a wonderful job. This is one of the first decent flashes I've seen that make use of Flash's minor 3d capabilities. Kudos to you on that one.
Secondly, you did a good job making the action flow with the music. While it may seem relatively simple, there are a lot of people who have amazing difficulties getting sounds and video to flow together nicely.
And thirdly, the use of a storm here was well done. Firstly, in high-action scenes, it removed the need to animate every second. It's a cheap trick, but it looks damn good for a cheap trick, so it's on the good side.
Overall technical execution: A
However, my review starts to get a little mixed around here, mostly due to some things I saw which I didn't agree with. For the storyline, you seem to have combined the original LoZ and OoT, which makes not only for a very inaccurate combination to the Zelda storyline, but reduces your credibility in adding your own chapter to it... but I have seen much, much worse, so no worries on that one.
Also, the use of final fantasy music in this film may have been effective because of the flow of One Winged Angel, but when I'm seeing a trenchcoated Gannondorf and Link with black hair in a business suit duking it out with swords, I don't think hearing "ESTUANS INTERIUS, IRA VEHEMENTI, SEPHIROTH!!" quite fits the scheme, although the tune itself minus the obvious tied to FF7 fit.
Continuity: C+
Which nets you a 4 vote and an 8 rating. Not bad, since I'm usually an ass when it comes to voting.