An interesting tale you have woven good sir
Well, well, well... where to begin?
Let's get the worst out of the way. The art and animation. It needs work. This is to be expected from a young artist like yourself, so I trust that in time you'll be making great looking animations, but as of right now, animating and drawing people seems to be your greatest weakness. The backgrounds, tech and general feel for the world they were in was great though.
Voice acting could use some improvement, but I'd understand that you're utilizing what you have to the best of your abilities. In the mean time, I know you asked for help on this in your comments, subtitles would be great to have and prevent me from feeling that I missed something important that was said or misinterpreted it.
The universe, or "omniverse" that you have created is top-notch. Unique, intriguing, beautiful, complex, believable, alien, and yet familiar. Avatar's got nothing on this. Not only are the well thought out omniverse and beautiful world's amazing, but the factions, and people in them have been equally well done. The political tensions remind me greatly of Cold War spy games, and proxy wars, as well as Ancient Roman politics. You have obviously put a lot of time and effort into the creation of your "omniverse" and it most certainly deserves more than just two flash movies.
That was just the world your story is set in, and it gets me stoked and wanting to explore it. The story itself is not as strong as the world it takes place in, however, we only have half of it so far, and it IS a good story. The writing is good, but not great yet. The potential is there, I can feel it. And I mean serious potential. I really want you to do your damnedest to bring your writing to the next level, because with your ability to create such amazing worlds you have the potential to make amazing epics to rival even the greats.
Cinematography was excellent! It's effect was weakened by the quality of the animation, but you can't get much better in this regard.
Music, was good, uhm... what else? Just DAMN man... Have fun with this you know? I really want you to go somewhere with this. Write a book, graphic novel, something. You CAN make money off of this, and with 100% honesty I hope you get a movie deal or tv series for this eventually. I would love to see it.
Great potential my friend. I can tell you're going to grow into an amazing story teller.