There were a few things that got to me.
First of all, the way you used the music. The music didn't quite fit in with the flash. You just played the tracks over the flash without them fitting in to well with what was going on (except for the sadness and sorrow one which fitted in nicely). It felt to me as though I was listening to my Ipod whilst watching the flash, and the music and animation just didn't quite go together (I actually have final destination and Show no tears on my Ipod, though that is irrelivent.)
Secondly, I can clearly see that you are a very good sprite animator however there were a few parts of the animation where I just thought; 'Meh'. The fight scene was where I felt this the most. It felt more like turn based combat rather than a proper fight at some points (although you did an excellent job on some parts). For example you had sonic & Mecha sonic running side by side for about 5 seconds. That was pretty boring fight wise. To make stuff like that more interesting, maybe have mecha sonic shooting at sonic whilst sonic dodges the shots or something along those lines. In a fight to the death the fight should be epic, and I know you have the potential to incorporate better stuff into a scene like that.
Finally, the drama with falco and sonics transformation, just wasn't very dramatic. You may have chosen a good song, but the whole thing just didn't seem believable, neither did it feel entirely sad. I think it could have been improved with some more sound effects, for example a cry of pain as falco is obliterated.
These are just my thoughts though. I'm probably being a bit harsh with my review; I know I'm no animator, and I've also been stunned recently by the brilliance of SMBZep8, however I'm sure you can understand why I can't give you a 10 with something like that out there. Keep up the animating though, its obvious you have great potential.