Haha well sir I applaud you! I noticed many many references to my original series, from the intro recap, to the scene references like the Super Light Speed Attack.
Your animation is nice, seeing Nazo's spike flap through the air when his flying is more than I did and touches like that really help. However I recommend working on your fight scene animation, you seem to lack the "oomf!" of punches and hits. For instance every time someone got punched, the fist would hit the head/body and they would remains still, like a rock. To really show an impact, we need to see physical effect of such a punch, by having a head turn, or a screen shake, or the entire body lurching from the force of the blow. You analyzed my movie very well, but analyze martial arts films, or hell DBZ/Naruto clips to see how they achieve that level of strength
Also, awesome that you got Omahdon to some voices, I say get full voice actors instead of text. I know it's more time consuming to do lip sync, but it grounds the character so much more she they have voices.
I am surprised you went through so many transformations in this one. I know my 3 part series was able to stretch it out long enough that I could give the normal and super forms more screen time and I totally get if you are not trying to animate as much as I did (I have no idea how I did that purely on spare time!!). If it were me I would not have had him go Dark Super Sonic again, I only did that for effect since Tails was supposedly dead, I would expect this time around he would have more composure. Same with having Super Shadic come in so quickly, I had it so Hyper Shadic was last ditch ,dues ex machina technique that could only be done in Hyper Form, but I still like what you have done with him and I am looking forward to the next battle.
The new things you brought to the table I like as well. The extra sensory abilities Mecha Nazo has now are cool, and his ability to manipulate energy. Can he still use Chaos Control? Also when making energy blasts, try to make them Movie Clips and set the blending mode to "add" instead of "screen", makes the energy look "hotter".
All in all job well done! I am most certainly looking forward to the sequel and I am glad you did not scrap the idea. Spruce up on more believable animation techniques and story spacing, and though if I went in one direction with something, you are not restrained by my decisions, have fun with it!