Excellent start
Well, everything was beautiful about this little Flash cartoon. First critique, however: some of the scenes dragged on for quite a while. The fact that the music and/or sound effects weren't always synchronized with the action made the scenes seem even longer (i.e. the music/sound effects would play at a consistent rate, but the actual scene would lag, making the sound clips end sooner than the visuals).
There should have also been some buttons to move the viewer forward in the Megaman briefing, just as there had been for Samus'. Instead, the text screens were just timed, and, I understand you were trying to keep it on there for quite some time in case some of your audience members may have been slow readers, but without the option to move to the next scene manually, it went right back to that "the scene drags on for too long" problem. Maybe you could go back into it and insert some buttons.
With those minor criticisms out of the way, however, I really, really wish more people at Newgrounds would make this sort of thing. A lot of movies are bottomless, worthless shots at humor or action, and they're also short to boot. They're not fully satisfying. But this movie was a good length, and the plot involving the two popular video game characters seems as if its going to blend into itself beautifully. It's tough to pull off a good crossover; but I am really looking forward to seeing where this is headed.
Great music choices, and great artwork as well. I can tell you worked very hard on this.