Make bombing more complex, and add more types of bombs - dropping in a load should be a real skill. I mean, flyable. If you don't think there's enough gameplay in just being a Destroyer or 'Vette, just play Independence War for a while. Landings in and taking-offs from fighter bays in big ships. Ignore the fools - capships have their flak cannon and beam turrets already.
Shields belong on happy little fighter people.
Return turrets to bombers, and let us command them via the Comms menu. It'd be fun as all hell. The return to the homeworld had better be impressive. Or perhaps Earth is lain ruin by the isolation and lack of imports. Make the medal-granting system better.