Which faction is stronger for PVE endgame? That should probably be the deciding factor.
From a looks perspective, lightning > little rocks. Conversely, nearly all endgame Assassin PVE and PVP gear looks awful. Luckily, however, you can get 4 piece set bonus without using body slot (and put something better looking on), hide headslot, and then you're left with inoffensive hands/feet and a silly skirt until you're at a point where you can customize your look however you see fit.
Consular gear isn't any better, IMHO if anything it's worse O.o. Since I'm just now coming back to the game and I was moved to a new server by Bioware, I have no idea the difference in progression on either factions, I can tell you that both sides see about the same amount of people on the main fleet at any given time.