One of my absolute most favorite features of Starfleet Academy was the damage system. It was fun to be able to take out a Klingon Supercruiser with my Federation shuttle because I knew where its weapons were.
I think that if you want a complex damage system that "works," you should check out Starfleet Academy. The way they implemented it, you could either attack as if they had a fixed rate of armor (like in VO) or target specific systems and aim accurately. (The exception was the Klingon/Romulan cloaking ships... if you didn't take out their cloak at your first chance, they'd simply cloak every time you got a bead.) The interface was pretty smooth, too, no need for a map of the enemy vessels or anything horridly complex like that.
-:sigma.SB

These threads may be of interest:

http://www.vendetta-online.com/x/msgboard/3/3242
http://www.vendetta-online.com/x/msgboard/3/8090