Well....hm...
Ok, to be brutally honest, cause thats what I do. This had its improved parts from your first flash with megaman, and its worsened bits.
Before I get into that I wanna give ya props on even making the damn thing. You had some decent amount of complex stuff going on in there that must have taken a ton of hard work. And that you even know how to make these guys walk smoothly is a credit to be given to. So as a flash, its perfect cause there was no malfunctions or error's in movement or anything. It all went smoothly. 10/10 for the process of making a flash. (NOT counting sound)
But where you really didnt meet par with this on was plot and what went on during the fight. And music...though fantastic pieces on their own...most of the time it didnt work for this. Which is fine, it may wor better for the people who adore all this music (i like it myself) so it makes it cool for us but in general it wont work for most people the way you placed it in for scenes.
With music and sound, use more of the megaman stuff or something thats not so...hip hoppity. The jumping sounds from Chrono Trigger just kept reminding me of mario for some reason...it took away from the action type feel and made it seem more...wimpy. Hard to feel all hyped up from a fight when your thinking about a fat plumber everytime they jump. I know its probably hard to find some decent quality sound files to fit what you have going on in the flash sometimes but spend a little extra effort (if you have some to spare) finding them if you can.
And finally...plot...alot of the action that you put in was great to start out with. But in the first one it seemed more even...and megaman had to pull out a clever comeback like rush to win against his enemy. In this one...the improved version of the clone didnt seem to stand a chance and all mega had to do was take a second and BAM. So it was kinda....blah.
And when the robots all gathered about him...a huge twist from reality. It can work though...just dont use so many evil enemy bots and focus more on the neutral types...like the monkeys or friendly droids. More enemys gathering around mega just does not make much sense >.< But the concept works.
So when it came to plot and music...it feel just below. I saw improvement from your first in action and such...but it really wasnt as good with plot. So a decent 7/10 for plot, and thats being generous.
^.^ But hey, at least you made a pretty nifty flash that isnt complete crap. Hell, you even got an award for it. So feel proud, take a small break to look up some ways to imrpvoe, and come back with something even more kick ass.