Meh.

Well...

This was... passable, ONLY passable.
As a sprite movie, it is bad, people who diss sprite movies do so only because they dislike the way it looks, but the good ones do exist, this... unfortunately, is not one of them. First one comes with the images, in which the sprites are JPEG, unusable, and often awkwardly stretched.
For an animation, it is also faulty, it is not smooth, slow, and unrealistic in so many ways.
There is no plot, there is no story, and there is no explanation as to what is happening, for an animation that seems to be well received, it's lacking substantially in what the people credit it for.
Appearance: This does not look that great, very harmful to the eyes.
Sound Effects: Dull and taken right from the game, not bad for what it is, but wrong game for the world.
Music: Almost no music, horrible.
Animation: Delayed, from what I can tell, it really needs a lot of work. I don't know flash so I can't help you with that, but that's what I see.
Sprites: Yeah, ones from the game, animated poorly, please try harder to know what you're doing with them and have them with better pacing.
You should be very careful with those who review your animation. Don't listen to people who praise an aspect of it without at least pointing out how it can be improved. If you're going to write out a story for this, be sure to look up the information yourself and to ignore what the reviews say, the Super Metroid sprites don't look good next to MMZX sprites and MMZ sprites. The images left a lot to be desired in how boring they were and how poorly set up they were, but you can fix that easily, I hope.
Oh, and this idea isn't that original, as a similar idea has been implemented in the past, with much greater execution and receive, be sure to check about things that already exist before trying to create your own.

maybe...

first let's have a look at the animation well it was ok it seems somehow low quality
the motion were good not bad but the battle was very boring samus shoots and then the other one shoots weeee the story is original though and you should do this but don't make the battles only shooting it's boring

its a pretty good sprite animation

but there are a couple things about it, one of them is that this flash has no preloader, which makes it slightly annoying if your wearing headphones on high volume. almost feels like your ears are gonna bleed because of that explosion in the beggining, the other is that that isn't megaman. from what i know from the megaman series, that was either gray or it was protoman, im sure its either of those two. the last thing is this has no storyline to it. a pleanet(?) blows up, samus kills a green dude, samus kills a blue dude, protoman/gray shows up, the place that their in blows up. it doesn't say anything about what's going on, what could have really helped is by putting in a text bar and typing what they say in. that would have helped out a huge amount with the story. but in rambling now so in short. good sprite animation. No real story involved, and a text bar would help out a lot. good luck on future submissions.

Effort is there, at least.

I have to give you credit. This is really a step up from crappy sprite movies, but... that isn't saying too much. At least you got the sprites working without awkward movement, but there wasn't much action. It'd look much better if you had several explosion sprites everywhere instead of one explosion that just grows past its native resolution. There wasn't much plot. The movie is pretty short given the size. If you could make the flash run at a higher FPS, that would be helpful. I suppose the looping is alright given that this is just an advanced "test" flash.

On top of everything, main character clashing would be a definite plus. Just keep trying!