As someone who has played both Assault and Gunnery, I can tell you that both are very effective in PvP, though either way a Commando is certainly more challenging to play than Vangaurd because, I think, all our defensive abilities lean towards active vs. passive.
I ran Assault from recruit gear to almost full war hero, and, unless my team was getting rolled, would consistently put up 350 to 450k in damage. I just switched back to Gunnery cause I am playing more PvE, and after a week or so of playing and tweaking my talet tree, I am back in the 300k to 400k damage range, and getting better all the time.
When I play, I make generous use of Plasma Grenade > Mortar Volley on groups, and combined these hit for 4 to 6k+ per target. Not a kill, but alot of pressure on enemy healers and of course makes people scatter, cancel cast, etc. Sticky Grenade is an excellent cap buster before you die (delayed AoE) and of course the spamable Hail of Bolts is great for preventing cap or scattering healers, or other casters. AoE is probably Commando's biggest strength.
Getting back into Gunnery, I find I have slightly less mobility (one less Instant than Assault) but of course Assualt can DoT on the move and therefore make targets vulnerable to HiB on the move as well. But, if u are running around trying to use that instant (Incendiary Round) all the time, you'll burn up your ammo real quick. Of course as Assault, Hammer Shot also can apply your DoT, so you end up spreading around a lot of damage when that procs. However, once you get into Gunnery, which I feel I am really starting to learn, you can really start taking out single targets, in a way that Assault always felt lacking. When I proc Curtain of Fire, Full Auto hits for huge damage... Like 1200 to 2000 per tick. For 3 ticks! And Demo Round with 2 to 4 stacks of Grav Vortex: 5k+ easy.
When it comes to staying alive, Tech Overide (long cooldown, I know) plus Medical Probe is ur friend. Combined with Charged Barrel you should be able to hit yourself with 5 to 7k in heals in 1.5 secs. Combined with our shield and Adreneline Rush, I rarely get killed in 1v1s vs. anything. Root (stock strike) and kite with hammer shot melees when they have a bubble or other def cooldown up, and wait till u see them start taking damage again to use your big hitters. Don't waste your high damage/ammo rotation on a Mara with 20% health u just knocked back and is now walking towards you with 99% damage reduction, only to ping away at them with Hammer Shot once they get in your face and Ravage you because all ur stuff is on cooldown or u are out of ammo.
So, again, Commando is very viable and has a lot of utility in PvP. You need to be able to switch between single target and helping ur team with all our AoE (i.e. drop it on the melees who are beating ur healers). You need to use your self heals, or use you heals to save a team mate. You need to spread around and apply DoTs with Hammer Shot as Assault, or debuff armor with Grav Round as Gunnery, and not just on ur target but on ur teammates as well. Have a good healer on your team? Use Tech Override for instant Plasma Genade instead of Medical Probe. You need to cleanse DoTs from pyros, etc. (I actually saw someone say our cleanse was useless!! What?!? You like burning and taking an extra 1.5k in damage while u run through the tunnel in Voidstar???) It's hard to play Commando well, and perhaps that is where it got the weakest advanced class perception, but well played we are as good or better than anything else.
EDIT (because talk is, as they say, cheap):