Let's go this chronologically through.
-The intro-
It's way too long for my liking. It fits as an ending better. But the animation itself wasn't too shabby.
-The first battle-
Funny, how Shadow simply bashes into the fight and laser-cannons the bot into junk. The animation here is a bit sloppy.
-The next battle- (Against Gizoid)
I've noticed, that the spindash is really useless compared to the homing attack. You have no reason to use the spindash, because the homing attack does 2x damage anyway. Think about it.
The animation's getting better.
I spotted Solid Snake. I wonder, what his role is in the story.
-Finished Sonic's story arc(?)-
Needs a skip button. Just a little thing I recommend. Many people don't have as much patient as I do. Especially if it's that long.
-Watched Shadow's story arc-
Yep, more animation is involved here. Overall, at your level pretty neat.
Let me get to the mini-game though. It's...hard to beat at first try. The button isn't well placed and not clearly indicated. You should some sort of signal, so people have some time to react.
The idea was there, but the execution of that said idea was poor.
My rating: 4/5 simply because... Yeah, this type of flash animation is really hard to make. Especially for your first. Your dedication alone impresses me.
Keep it up!
tl;dr version: Awesome flash, but your gameplay needs some fixing/improvement.