Well...
The art is fantastic. This is one of the most unique things I've seen on Newgrounds in my 5 years of visiting this site. In context, it seems like something completely out of another world. It isn't, of course, not if you've seen German expressionist woodcuts from the 1920s. But it is very unusual in this day and age. The animation was also done surprisingly well.
The music fit the film well, although I did not find it to be memorable.
I think the biggest problem here is that we are given little reason to CARE about what is happening. You introduce a bunch of unknown gods who are promptly either destroyed or transformed, and the only thing you tell us about them is that some are "good" and others are "evil". Why should we care whether the "good" ones win or lose? What hangs in the balance? Basically, who are they "good" FOR? What some may call "evil" is also beneficial for some, so it is hard to take the narrator at his word.
You've succeeded in making it be "epic", but epic things need to be grounded by something that feels real; for example, LOTR was grounded by the hobbits and Sam Gamgee in particular. The Greek and Roman gods exhibited characteristics that were well-known archetypes to the people of the time; something to relate to. Lynd Ward's woodcut novels of the 1930s, while being dramatic as hell, spoke to issues that people could relate to.
You need something similar, I think.
Also, on another note, try to not have the film automatically repeat from the beginning once it fiished.