You need to rework this heavily
Ok, while I can see you tried to do a good flash, there were plenty of faults. Firstly, you broke from your overal flash story (which is supposed to be Zero versus Link). Very early into the flash, you break your own story by throwing in Sonic, THEN metal sonic. That doesn't even make sense.
Now, sounds wise, you have a problem with the song dreams of an absolution in which it should stop once the credits are over. Instead, they keep playing EVEN WHEN YOU REPLAY THE FLASH. That's bad.
Also, your sprites were horribly squashed. They should always be their correct scale whenever possible. I also advise you choose a better sprite set for Link, as it did not look nice at all. Even the spin attack looked rather bland (you should have at least four versions of link's sprite to spin between when he's doing those rotations)! You also need to learn PACING with sprite animations. Super Sonic's arrival had him jittering about like he was high on caffine and sugar at the same time (and that is nooooo good *shot for overused meme*).
Overall, you really need to take this back to the drawing board and rework on this. I know you can do better at this if you just TRY.