I DO agree that the empire is more "interesting" and has some small move advantages. However, I would like the stress that this tends to be a common occurrence and might even be inevitable in dual faction MMO. For example, in Rift nobody had a clue what the lore was, who were the good guys or bad guys, and all the classes on both sides were the same. It was Defiants vs. Guardians, but that might as well have been Red vs. Blue. However, while it was balanced at first, Guardians started becoming stronger and more populated and it only snowballed from there. Maybe all it takes is a well organized PvP guild that dominates a bunch of warzones that then frustrate players on the other faction into thinking they should switch because they're on the losing side. Then there's a drop in population and the imbalance gets worse and worse.
One thing that helps this is long queues on the advantaged side which makes it boring and slows gear progression; however, because of huttball in this game there is little incentive to switch since you will always have someone to play against. The addition of new intra-faction warzones only makes this worse. I commend you bioware for a creative, good idea, but it does remove the incentive for faction balance. This may or may not have lasting consequences.