This is a tough one. Pulse rifles do have the upper hand but they do take a bit more skill to use. Not much however. I don't like them nut today I used the test rifle and within a few minutes I was wrecking people and even won inferno rumble which is crazy for me since I don't play pvp that often and never use pulse rifles in pvp.
I consider myself decent with an auto rifle but I could hardly beat anyone using a pulse rifle. I would get them to almost dead but they would generally win.
Point being is that something needs to be done to make it more of a fair fight so that players can choose their weapon of choice but I am not certain what.