On the note showing target boxes for you to shoot at to damage systems perhaps this should be limited to very advanced craft. Only certain ships have lead indicators so make it the same with these disabling targets.
I don't think that most craft should have targetable systems - Most are too small for stuff like that. It would be a giant clutter of targets. Bombers, TT/HTTs, Stealth Bombers, Gunships, and Capitol ships should be the craft that should have separate targetable items - Capitol Ships more so than the other ships.
And for one destructable item - The 'Cargo Hold' - Do enough damage to it and it ejects the contents.
The only problem being that all 'turrets' occupy the same spot in the center of the ship. Making them targetable would mean that they would have to have spots on the hull, and then add in limited firing arcs, possibly more models.... It would be a HELL of a lot of coding.