It was...alright...
There are a few mistakes, but it's pretty good.
Graphics: Probably the worst of them all. I noticed you mixed bitages with the Vile vs. Megaman. Though unavoidable if you wanted that fight scene, it's almost never a good idea to mix bitages. However, for a non-spriter, it may not be that noticable. The stuff that was drawn fit in very well.
Style: This got hurt a bit as well. Though I believe it was purely unitentional, some parts of this closely mirror the "Mega X" episode from the old Megaman caroon series.(Megaman getting his but kicked by Vile, X appearing to save the day. althoughSigma came personaly with Vile instead of Spark Mandrill)
Sound: No problems here.
Violence: ot that the 10 I voted for this does not mean the amount, but how it was used. I believe all the fighting served a good purpose in the plot and turned out very well.
Interactivity: I loved the DVD style menus and bonus materials.
Humor: Pretty funny at times, but much better placed than the last two movies.
Overall, great job!