I think the biggest problem that people are experiencing (yet overlooking) in pvp is lag. What may look like bad weapon balance is often times just due lag. It's been the case with every game that suffers rubberbanding/lag that low fire rate weapons suffer significantly more than high fire rate weapons.
You need three upper body shots with a scout to kill. If lag causes you to miss one shot you are at a more severe disadvantage than if you were unloading 500rpm into someone with an auto rifle. I have found that sometimes I open on an unaware opponent with a scout rifle headshot, take them down to 40 percent immediately, and still lose to their autorifle due to the delay to the followup shots. It's even more difficult against those who strafe. You will notice similar results with pulse rifles. The lower the fire rate the worse it will feel. I have found that higher fire rate/lower damage pulse rifles are more reliable in pvp.
As far as my thoughts on actual balance:
I feel like between scout and auto it is close to where it should be. Auto rifles have an advantage in close quarters and to stand a chance with a scout rifle requires headshots. In the long range scout is better but not by a lot. Auto rifle is almost just as accurate at the long range and needs a tiny bit nerf in range or damage drop off especially since most maps are close/mid range.
Pulse rifles vary greatly depending on their fire rate. I feel like they are lagging a little behind and should receive a buff to fire rate. This should make them a bit less reliable than a single shot in the very long range and a bit more reliable in the mid/long range, placing them in the space between auto/scout.
Handcannons are terrible and needs a complete rebalance. It is not good enough to have a weapon that doesn't excel at anything. As it stands it is weaker than a scout rifle, which already is outclassed by the auto in most situations. You can make it more difficult to use by lowering fire rate/adding a significant amount of recoil, and make it kill in two shots to make it competitive. Or you can go the other way and let it kill in 3-4 shots, but make it fire as fast as you can pull the trigger, the weakness being range/recoil. It needs a space/situation/playstyle that it is great at for it to remain competitive.
Shotguns: It is fine that they can kill at point blank range and I feel that it's fair because the fire rate tends to be low on these. You have tools to stay out of it's effective range if you know someone is wielding it. I find that I am inconsistent with it so I generally try to avoid using it as it is difficult to use if you are not absolutely point blank range.
Fusion rifle: This gun can vary from absolutely useless to pretty damn good depending on the stats. Ones that charge a long time are fairly difficult to use, yet those that charge up quickly are like a shotgun with a little more range. I think those are pretty underused and I'm glad that finding a good one takes a bit of luck.
Snipers: Classic Halo balance. Two body shots or one headshot. I can't complain too much since they at least removed the reticle outside of ADS making it a little bit harder to quickscope with.
Heavy weapons: All are strong for PVP and PVE as they should be.
Overall guns: If you look at the guns you will see that every weapon can be at a severe disadvantage depending on range except for the auto rifle. It works well at any range and can often beat close and long range weapons at their respective ranges.