I used MK6 dual heavy cannons on a Tier 3 Klingon ship, Weapon setting 115, klingon was camping so full of energy. I used Beta and Omega 2/3 pattern, fire on my mark, rapid fire 1, imp Torps 1 9/9 by the time my Mk3 (with +20% anti disrupter) front shields been down the klingon lost O.O 4% shields. I was dead before rapid fire 1 was off and yes ... my explosion in him did more dmg then my assault on him.
From your own description it sounds like you only really use Offensive skills. I'd bet my BoP that your opponent was using some defensive skills, such as Reverse Shield Polarity, Science Team, Engineering Team, etc.