OK, so I've spent a LOT of time over the years watching and breaking down game and film trailers, both official and fanmade, and I've got some things I'd like to see which would go a long way to upping the polish on this.
1 - You've got a fair few good voice clips, but currently they almost all seem ill-timed because the person speaking rarely matches up to what is happening on screen. You have QAI speaking while you pan over a large group of Percivals, and other similar oddities. When QAI says the UEF is going to lose the war to the Aeon, you should show a battle between UEF and Aeon forces with the Aeon rolling over the UEF with ease.
2 - Without doubt the best SupCom video of all time is Angel Supreme. The things that make it great are the great music, music with orchestral instruments and a good beat, not too heavy on the drum, and a good, solid melody. In my experience, most popular music from the last 5 years has been crap for this, so I recommend finding a track from Two Steps from Hell or Audiomachine (I will go in search of tracks I think suitable). Make sure that your visuals are synced to the music.
Additionally, Rake picked clips which never ever seemed artificial. They almost all comprised of a good mixture of units in large battles, instead of the rather dull shots you have picked up of dozens of Percivals/Bricks/Whatever all lined up in a grid. That doesn't send a good message about what this game IS.
3 - For the Seraphim's lack of a voice line meaning you don't have their symbol and phrase, I suggest finding clips of the other characters talking about the Seraphim, and use those over scenes of Seraphim armies kicking butt.
4 - I've already PMed Sheppard with my thoughts, but what do others think of my ideas for the Seraphim and Nomads themes?
Aeon - Purity (Fits far far better than clarity, as the Aeon really aren't seeking clarity, they are seeking conformance from all to their religion)
Seraphim - Dominion
Nomads - Rebirth
I feel both fit very nicely into describing what the faction wants from its quest.
5 - In this age of fast internet and increasing graphical fidelity, prospective players are going to demand quality, even from a community project like this. As such, the final product must be produced and recorded natively at a MINIMUM of 1920*1080. For capturing scenes ingame I suggest you use Rake's method: He maxed all the graphics settings, including AA, then captured the game footage at -10 simspeed, then sped the footage back up to real-time in the editing software. This allowed his not-so-powerful machine to render the game at the best it can possibly look, with no hiccups, and meant even the very very largest battles happen in real-time in the video.
As an added offer, if you need any 2D, non-animated stuff doing, I have a fair amount of graphics manipulation experience in Photoshop CS6. I can't paint anything from scratch really, but manipulating existing stuff I can do very nicely.
http://aeoncleanse.deviantart.com/