Well, that was certainly a sizeable piece. I've got a few things to say.
The 3D effect was an interesting concept in theory, but in practice, here, the number of errors caused by the use of the 3D environment (lack of elements in outer edges of the frame, miscalculated depth, misplacement of sprites, low resolution textures on models) overwhelmed the benefits. Coupled with that, there was just something... off about the choreography. The movements of everything, dudes, weapons, vehicles, projectiles, seemed just a little bit too... slow. Everything seemed to be taking its time getting where it was going, and that's not lag, I'm on a gaming rig here and the 3D sections were running at 60+ frames per second.
Again on the subject of the 3D sequences, their visual quality compared to the quality of the 2D frame-by-frame animation really cheapened the 2D animation, particularly given the 2D animation was of significantly lower quality to begin with. If you attempt a splice like this again, I suggest you make an effort to have your 2D segments run at a framerate similar to that of the 3D segments, either by capping the 3D framerate or increasing the 2D framerate with more... well, frames.
Lastly, saying there's 'no actual protagonist or antagonist' comes off as really quite pretentious, given that the flash clearly featured visor guy and rocket-pack guy as the protagonists, and glasses guy with his army of grey guys as the antagonists. The protagonists may have been anti-heroes, but that didn't make them not protagonists.
But, despite all that, I really enjoyed the animation. The 3D aspect, while flawed, was extremely interesting and lent itself to some brilliant camerawork. Some of the content was just plain awesome - the addition of the body-consumer, Mr. Faceless, and Flaming Dude With Sword added a wonderful fantastic element that kept the animation from succumbing to Madness tedium and becoming just another bloodbath with lots of grey. Also, the music was fitting and well-placed.
Overall, flawed, but in the end, quite good and certainly memorable. If I were you, I'd keep working with that 3D engine of yours; see if you can iron out the quirks and give it that extra spunk. I'd certainly like to see more done with it.