Everyone's getting really butt-hurt lately...
First and foremost, to address the elephant in the room-- Yeah, making a flash movie to basically go and publicly tell the audience that his movie was crap and didn't deserve the fame is pretty low on your part. Especially considering that you yourself could've done ALOT better in my opinion.
Admittedly, we do the same with things like the Twilight series, but let me tell you one thing: You can't change public opinion, no matter how dumb it is.
If we could, no one would drink, no one would smoke, eat shitty food that would kill them, and everyone would be tree hugging, peace loving family of the Earth and nations. (Me being a "sinner" in almost all of these mentioned.) I digress, but sad to say it, as an entertainer, you play the crowd the best you can, even if your crowd is retarded.
Anyway! About the movie itself... Superb animation. Loved your art-style and care for detail, despite the short time frame you worked with. The music did get a bit irritating and redundant, including the voices-- which really should've been played up. Such as, the music should've gotten more intense per shot and/or different music played for each segment. The audio-portal is a vast, and bountiful place for music. The voice actress itself (btw, Kudos to ya Hnilmik) should've been directed to get frustrated with Link, or at least do different takes for each scene you did. I realize Navi is irritating, but I shouldn't have to hate the actress with her. I've worked with the VAC before, these guys are top-notch, and can do almost anything you ask, don't hesitate to push their limits sometimes, seriously. They may even need it for practice/their portfolios.
If you really wanted to go ahead and improve the original, especially by show-casing the many different avenues he could've gone down for the joke, I think it would've made a WORLD of difference if you actually connected each segment by making it into a story. I.E., each shot is from the same event, that Link is just sitting there repeatedly shooting arrows until he hits the twin-towers and tosses the bow and arrow to Ganon and runs like hell. For the most part, the repeat-set-up in such a quick jump distracted me and didn't let any of the jokes really sit long enough to be enjoyed. Although I did smirk at apple of Eden bit. You gotta lead your audience, don't keep throwing glitter at them hoping they stay interested.
In a nutshell, Animation and Art = Awesome, keep going man. Writing = Getting there, take a little extra time next time and maybe beta test with a small group of friends. Music and Voices = Seriously work on that, the wrong acting and wrong music can kill even the best classics. Imagine your favorite movie with your most hated song played over it on loop.
You're doing amazingly well despite it all, and you're on the right track. I checked out your page and I think once you branch off and do your own thing (maybe animate that web comic you got there?) You might be the new Newgrounds Legend. Been waiting for someone to challenge Egoraptor for awhile now. ;)
Best of luck, and hope to see more from you man!