The more I've thought about it, the more I've come around to the Funknown View of sandbox balancing - CE had it right, every game since has had it various levels of wrong. A single powerful utility weapon surrounded by a nimbus of more niche weapons is the way to go.
In that spirit, autos should have more distinct behaviors and interact with other parts of the sandbox to make up for their more simplistic/noob-friendly archetype. AR extending camo from CE is a good starting point. Then take the SMG and dial the recoil waaaaaaay up. SAW, I think it'd be a good idea to give a windup time and have it interact with Overshield in some way (as befitting its AR+ status). Suppressor, it'd be cool to have it do something like knock people out of sprint or lock down Thruster or something. Then add the plasma stun back to the Storm Rifle.
Accompany all this with a general damage nerf, so that precision weapon TTK is always higher, and I think you've got something.