It's a start, and a bit of a twist on the formula
First off, I've never seen a Mario flash where he is Megaman. An odd concept, but it actually worked out surprisingly well. Given Mario's many costumes and power up suits, I'm actually surprised noone else has thought to combine the two!
Made me nostalgic for the classic old Megaman games as well. I loved playing them back in the day, and using authentic music from them made the movie work well. It was even laid out like a decent level, which helped it feel fairly authentic to the experience.
My main complaint would be that it is just too small. The stage is about 80% empty, just a white void. Make the backgrounds and sprites bigger and fill up the screen. Everything is small and hard to see, and making things bigger in flash is simple as could be.
Hopefully for the next flash you do you'll have backgrounds that fill up the screen better, and action that doesn't require eye strain to watch. A very solid first flash though.
PS: Was I in the special thanks part of the credits? Very kind of you, and good luck on your future submissions!