Good... but not so good at the same time
First off, great job creating this flash, it shows that you definitely put a lot of work into it. The intro scene was especially great with the music and all that, very easy to get into it. I also like the idea of Link using an evil sword in the name of good, just makes him seem even more bad-ass.
Unfortunately, I'm a nit-picker, I'm very into details. If I recall correctly (which I do, just an easy way to start a sentence without saying "First of all again" :P ), Link went off to the east into the clouds to reach the dungeon, yet when he kicks the Faceless MJ Clown off the tower, he appears back on the map where the tower was in the actual LttP. Makes no sense whatsoever, unless F-MJ-C "teleported" him there on purpose (which would be stupid if you think about it).
Second off, as it was said earlier, LoZ has never had any blood in it, and it just doesn't seem "right" to have them getting chopping in half and having their heads smashed, or being thrown into walls and then slowly sliding down, leaving a trail of blood behind. It would definitely add to the flash if you just left it as it should be, where the enemies disappear after you kill them and make the weird little noises. Not really a problem, just seems weird, so feel free to ignore this paragraph.
Third, the whole thing with the sage saving Link after being "knocked out with one hit" seemed, well... stupid. We never even saw an attack, just the MS and the Dark Triforce merge, which didn't even look like it could be an attack. If they had merged and a beam of some sort came out and blasted Link, maybe heard him scream or something, it would have made a little more sense.
Oh yea, just another thing to randomly point out: Right before hitting play, on your little "recap" thing, it explains how the fire mage is planning on use the MS and Dark Triforce to contain (blah blah blah), and then out of nowhere it says "Zelda was also kidnapped by a mysterious figure". That's just seemed really random and out of nowhere, and if it wasn't the fire mage that kidnapped her, then it makes absolutely no sense at all, and shouldn't even be known as a mysterious figure, shoudl just say she was kidnapped. Something like, "Link, in an attempt to protect Zelda from a bomb, leaps to push her out of the way, only for her to mysteriously vanish, with only an evil laughter echoing through the air left behind."
Oh well, just my two cents, I know saying this won't change anything, but hopefully you'll consider some things I said for your next flash video... although I don't really know how you can put most of what I said into the next one, but whatever. As I stated earlier, it's a great video, you clearly put lots of effort into it, I like the story, etc, etc. Great job :)