the two factions would be cool, but what do you do when they both choose the same one? i think besides from the colour it should be random but it should be different since the two armies look identical and that doesnt make sense. maybe the outta appearence could be dependant on your country!
now that is a good question that i think can be easily answered
in the match settings you could have an option of say mixed/fixed teams and it would all be a matter of who is your fog of war and who isnt (ie current team matches) if your confused as to who you should be shooting at.
mixed teams: Pick what art set you want and let normal random team generating do its thing.
fixed teams: pick what art set you want, you will be teamed with other players who have the same art set.
but in the end i know that the developers ultimately decide whats best for our beloved battledex
btw, the country thing could be interesting. maybe if the player lives in america, his/her hq would have a lil american flag or a statue of liberty out side it or something, lol