Suggestion: Specific targeting of ship systems.
This has probably been suggested before, but how about the option to target specific parts of a ship?
For instance you could give the order to target a ship's engines, shield generators, or weapons - or just a general attack on the ship as it is now. Attempting to target a specific location would come with an accuracy penalty, but any hits penetrating the armor would be focused primarily on the selected systems. Say a 90% chance to hit the selected system, with the other 10% going to generic parts like crew quarters and fuel storage and engineer sections which might be surrounding the system you're targeting.
This way you could specifically target a ship's engines to either slow it down so your slower ships can catch it, or disable it for boarding combat. Or use mesons to focus on taking out shield systems of a heavily shielded ship in order to follow up with a missile barrage.
The accuracy penalty could either be a set percent (maybe 30% or 40% reduction) or be based on the ratio of that type of part to the rest of the ship. In the 2nd case it would be easier to target a ship's engines when a third of the ship is engines, but targeting the 50 ton engine on a 500 ton fighter would be more difficult.