The first thing i notice is the use of the Omega torpedo launcher in front.
While it is a good weapon, the real strength lies in the HYT and torpedo Spread.
The first reloads slowly and the 2nd is most effective in a 5km range.
In order to get max damage from an alpha strike you need to close to within 5km and after that you need time to get back on target and your firepower relies solely on the relatively weak rear turrets.
If you have access to it then i would replace the forward Omega torpedo with the Romulan torpedo or a Quantum torpedo for burst damage.
Place the Omega in the rear.
I also notice that you use the Isometric charge, but your boff powers are aimed at dispersing opponents while the Isometric charge is most effective when you can bunch them together.
Adding a gravity well would be advised.
With this set the best way to maximize your damage is to go slow and keep distance. That way you can keep your nose pointed at opponents. Almost a cruiser tactic (cruiser keeping distance and broadsiding the opponents).
If you like to get in close then adding rear firepower would be best. For shoot and scoot use the torpedo layout i mentioned above.
The first thing you want to do is switch your eng abilities to 2xEPtS1 with an A2SIF1, that will make you considerably tougher and eliminate some of your cooldown conflicts. Then drop TBR for GW, which is much more reliable and easier and safer to use. I would also say that you should think about dropping one of your torp abilities for a second attack pattern, either a Beta or a second Omega, and if you don't do that definitely drop Spread down a level or two and boost your cannon abilities (higher level Spread just means more targets, and it's not usually useful to hit that many). Also drop the cannon ability CD doff, you have literally no use for it in this build as you can't use more than 1 cannon ability every 15 seconds, and when it does trigger it only drops the cooldown to 22.5 seconds, so you're always going to be better off with using your second ability. I believe the Projectile Weapons Officer doesn't affect the Omega torp, so you can drop that too.
You definitely can do significantly better DPS than you've been getting, my own severely sub-optimal build (poor weapons, weak consoles, and no doffs) gets well over 5k in every ISE I run (actually, that was with a parser that's usually 20% low compared to the standard one, so I need to recheck that now that I have the right one). You can see that build here: http://www.stoacademy.com/tools/skil...Sussnni04_2511