I'm certainly not experiencing the same results as you are then. So far, I have literally had to pound the crap out a system in order to finally knock it out... and I KNOW that I took out the armor, shileds, etc. This is when I have flown klingon, using disruptors and the like. I have not been able to effectively fire one disruptor at a time to stun or damage any system. I had to alpha strike.
When I fly romulan, which I like most, I can knock out systems pretty easily, but tha'ts because one shot of plasma is a whole lot of damage. I don't have to fire everthing. But when I go disruptors only, one distruptor will not do the trick. I usually have to overload disruptor 1's or 2's in order to get a desired effect, meaning that my fight to take out multiple systems will take more time than I actually have to hurt the person significantly. He just faces the other shield at me and alpha strikes. Well, whatever, I'll just keep giving mizia a try. I'm just suggesting that the 'wrecked ship' effect of sfc2 is missing in sfc3, and while the games are certainly supposed to be different, I can swear that a lot of times a person's ship is destroyed, but right before that he still had the power to fire weapons, go full impulse, and use the warp drive. the only real disadvantage he was in was that he he had to repari his ship three or four times, and now his shields are down. Otherwise, he's an intact ship. At least it seems that way to me.