I second a lot of what's already said, especially with having a decoy turret for blue. Something more accurate than Gatling and more effective than lasers at destroying missiles, and could be balanced out with not being able to be used offensively in any capacity.
Rocket drones - yes.
A little concerned with the one-shot-kill type turrets as it seems only natural that the enemy should have this too, and I don't like losing that quickly.
I never feel willing to sacrifice a red slot for escape pod or teleport, even though they both sound cool.
Gravity inversion/repulsion blast: Disperses a crowd and helps you single out some ships. Or maybe some kind of weapon that triggers an enemy ships's warp drive and send them back to the sector from which they arrived?
Electromagnetic Pulse Cannon: Temporarily drops enemy shields, or disables their energy-based weapons, or disables everyone's energy based weapons.
Force Field Barrier: Emits a temporary field X units long which the enemy cannot pass. Helps put distance between you and close range fighter enemies.
Space Stations: would like to see more interactivity. Maybe there are some missions for hire available at stations? Or rumors about which sectors may have contracts?
User Interface: In the purchase ships screen, I would prefer to be able to see the red/blue/green slot breakdown for each ship.
Environment: Random wormholes that transport you off-map and force you through a few sectors of unbelievably hard battles with the Borg before spitting you back in your galaxy. Not sure how I'd actually feel about it, but it's an idea.