I was gunnery up untill 46 or something, having the same problem as you guys I noticed in pvp my survivability was woefully inadequate, sure we can dish out the dps but you have to effectively play sniper and sit as far away as possible otherwise you get attacked and destroyed by anything that moves.
I had a short stint with assault specialist, I found the dps was really poor and I still had the survivability issues I had in pvp and pve.
I then decided to focus on pvp more and go combat medic; it was the best choice I made regarding my spec and now all I have to do is optimize it a bit for pvp. I find in warzones I am more of a tank than any vanguards specced into shield, when i'm not taking damage I can catch up to and save the occasional ally and even turn the tide of unbalanced fights just by being able to keep myself and an ally alive while they dish out the damage. The downside is that as a CM I do very little dps, if i'm not healing myself when someone is attacking I will usually die which means I have no time to do any damage let alone the quickbar slots to dedicate to dps abilities when most of them go to heal/survival/CC cooldowns; hammer shot with 30 stacks usually deals a respectable amount of damage, so if i'm lucky I can finish off an enemy or throw the odd plasma grenade into a group.
Not that being unable to dps is a complaint, I waived my ability to dish out damage in favour of survivability and being able to heal my team, this is definitely a choice I will be sticking with in the forseeable future and I would recommend it to anyone sick of the squishiness of the commando dps specs.