This is just my 2 cents here, and I am preparing for the backlash of this statement...
I have a level 50 merc and am in the process of leveling a sniper, both of which I pvp heavily on. Even at 16, my sniper is topping the damage charts and is on-par with my BH, you just have to play a bit more conservatively. However, this could change at 50, just because of the difference in gear/experience of the players i'm fighting,but I will also get better gear/experience with using the class.
But as it stands, both are a blast, and both have excellent stories. It is all about personal preference, and, believe it or not, the classes are more balanced than the baddies on the forums want you to believe.