Ach, the usual. Have the Engines, guns, (computers/crew?), (fuel and/or ammo storages?), special abilities like tractor beams or tachyon emitters, and also the armour as components that can be gradually reduced in effectiveness or outright destroyed; similar to the engine damage system - but less dependant on the attacker (since right now, you need to have special engine damaging properties to deal engine damage. Huh.), and more on where the shot hits.
Of course, that's all complicated, and realism junkies like me will have to concede that AIW isn't exactly realistic in the first place.