It's all about Perspective.
At first, I was a little weirded out by Sephiroth's One-Winged-Angel theme, but as you said in your description, it does fit the mood.
Positive feedback: I absolutely love the character design. Not necessarily that Link was in a suit, but it's a refreshing change of scenery. What I speak of is the fact that you did this in Flash, and Link looks startlingly 3D. I couldn't do that in flash if I wanted to.
Negative feedback: the only thing that rubbed me wrong was that Link, in all of the Zelda Games I remember, has always been left handed. I'm not a lefty, but i think a main character who is left handed kind of adds a touch more uniqueness to his persona. Another famous lefty is Sephiroth, the villain whose music you used.
All in all, I give you a 10 for originality, a 10 for visuals, a 7 on the audio, and a 5 for nostalgia. This was a very good flash.