This has been a trend in faction based mmos for awhile now. It was brought about by the perception created by WoW. That being that the so called "bad guys" are always underpopulated, but generally populated by better players.
Now too many nubs want to look like they're "leet PvPers" that "play the underdog", and the balance has shifted.
The key thing is for BW to stay the course and not make any knee jerk changes to the game to balance the factions. Like in DAoC, things will work themselves out. Either enough people will re-roll the underpopulated faction, or the players of the underpopulated faction will step up their game to the point where the imbalance doesn't matter, or a mixture of both.