My guys really don't like the disparity in the rule sets between small/large ships and huge ships. If you look at every video game and even movie released, smaller ships have more of an impact than thought on these huge ships, especially the smaller huge ships we are familiar with.
I easily envision a huge ship being given an out line with certain sectors and weapons having compartmentalized sections of Shields, Hull, maybe weapons, maybe a very simple repair round at the end of the turn consisting of a D20 roll and a chart.
Basically, you have a squad connected unto itself with some tricks up its sleeve and escorts.
If anyone has this idea fleshed up, please pm me. I'f not, I'll work on it and make it available.