It looks pretty slick, although I am a fan of the charged Mega Buster shot. As awesome as MM2 was, I don't think it was due to the lack of a charged Buster.
The levels certainly do invoke a sense of familiarity on various screens. If that was your goal, then I guess it's a good thing.
Suggestions:
1. I think you'll find that having Rush fall through the floor is more efficient than having him attempt to materialize, then return to the "sky" on a failed attempt. The way you have it now takes a second or two longer, and while your way matches the MM3 animation, I believe they changed it to have him fall through the floor in MM4 and 5.
2. The stage select looks awkward with Megaman slightly off-center. I'd suggest a different layout -- one that puts Megaman in the center of the screen, even if he isn't centered vertically. Also, there's no need to have Megaman's head AND the Dr. W stage icon. Remember how they did it in Megaman 3?
P.S. - What's up with the title? Isn't that the same title that Transformers 2 used?...
Anyway, I would definitely like to try your fan game once it's finished. Nice job following through and finishing a preliminary working level.