I'm not sure if this is too out of scope for TA, but I'm going to post anyway. Maybe it'll be remembered for GalCiv III.

I'd love to see destroyable ship components. As a ship takes damage it really would be cool if it could loose it's capabilities. Couple that with a basic targeting system where you could say, order your ships to target specific main components like engines, weapons, life support, etc. You could reduce the % chance to hit when such orders are given based on the component targeted. You could even factor in the sensors somehow. The better sensors you have the better chance at hitting a specific component.
That's a lot to ask...though. I'd be happy with % chance based on amount of damage taken to destroy/damage a random component. That would make chasing down a big battle ship with masses of fighters more fun. You'd have a small chance at knocking out the engines or some such, thus crippling the battle ship.

Just a thought....