Where to start...
First off, I read a lot of the reviews that people posted. I read all the reviews that you replied to. What I noticed is that you are taking everyone's criticism very personal, and in turn you're making yourself look ignorant and like a jerk.
The story wasn't even close to the official storyline. So many problems in so many places. I'm sure you could have gone to a dozen Mega Man X fan sites and got a good general summarization of the beginning of the X series.
I don't know anything about Flash. So it really isn't my place to judge you on your animation. But since I have been coming to Newgrounds for five or six years now, I feel like I can say that you need to work even harder. Two years and this is the product? I'm not being sarcastic when I say this, but what took so long?
The voices, as everyone else pointed out, was probably THE worst thing about this movie. Personally, I believe Sigma sounded ridiculous. I'm not saying the V.O. was shotty, but its SIGMA. And he didn't sound threatening at all.
In turn: I can see a bit of potiental, just keep working on your craft.