Enjoyable, but Missed the Sweet Spot
First let me say off I never felt like I was entitled for something during the 4 years you were working on this. You worked on it when you could little by little, I don't understand why that is so hard to understand. Maybe these complaints are coming from people that don't have to worry about working/going to school/doing things besides animating?
I will say that I was astonished by the trailer. It was before I was done the 3rd part of Nazo Unleashed and I was like "wow this is so much better than mine". That was 4 years ago, so Newgrounds' standards of "great" animation has increased and people have matured (imagine the difference of opinion of someone who was 14 and who is now 18). As of now the score is 4.04, which I am actually surprised by how low it is. Had this been released in 2006 or so, you'd be in the top 50.
The animation quality itself. A HUGE jump in quality between Act 1 and Act 3, but you improved as you went on so it's understandable. You used a lot of frame by frame which I can respect. It really shined on Sonic's battle on the egg carrier. The missiles were done well and The Chaos 0 water was also nice. You should take more consideration in to 'anticipation' poses. Like when Knuckles threw the asteroid, unless that was a comical choice, seeing him wind up the throw would have had a better impact. Remember that any movement you do to go forward requires you to go backward first, so jumping out the way of an attack requires the character to crouch so he can spring his legs to avoid the danger. It was a shame to see a nicely animated scene when Sonic drops on to the Egg Carrier, but when Super Shadow shows up, Sonic stands perfectly still and injured, and only his arm moves to back hand Shadow away. Again, It would have looked much better to have him wind up.
You also tried moving character in perspective, which I applaud you for, but I spotted many distorted perspective drawings (the dock not aligning with the horizon was one but again it was Act 1). When Super Sonic fell off the ship (can't he fly by the way, why worry about falling :P) looked a bit odd, and it looked like you had trouble staying on model. The character proportions changed a lot. Much moreso in in Act 1, but Knuckles head size/quill length was not consistent
Story? People these days seem to LOVE THEMSELVES SOME STORY. This could have been done without a story and been fine that way, however, you did imply a story, as if Sonic failed, Shadow ,Chaos 0, and Eggman would destroy the world. A triple pair up like that definitely warrants some explanation, but it was entertaining to watch unfold. A shame Tails could not have done more. You took the time to model the Tornado 2, I would have loved to see it attack the Egg Carrier Sonic Adventure style! You could have did without the cringe-worthy anime stereotypes such as shots when we see one eye open/close (I am guilty of this myself!) or seeing Knuckles in a cloak, which actually seemed more like a Full Metal Alchemist power than super strength.
However, my biggest issue with this animation is the pacing. You chose to have it musically driven and not use sfx or voices, which is fine, but the music only matched the Act 1 somewhat. All the other scenes seemed to be action with music thrown in. I love Guilty Gear music but by Act 2 it felt very out of place. Chaotic Battle worked very well with the GG music because the music complimented the action. For instance, you used the awesome track "meet again", but when the shot gets to the missiles firing, the music is still very slow. Action cartoons combine good choreography, camera work, timing, and sound to get that "oomf". The thing is, your *trailer* was synced very well in terms of action and music, with audible cues connecting the actions on screen. Seeing Hyper Sonic punch shadow had minimal impact without a beat/sound effect to back up the punch. I'd go as far to say that you should add some slower scenes for pacing and coherence add sound effects, that's just me.
Running out of character space! At least you are finally done! congrats