Precision Gear - I don't think it's currently possible to give bonuses to specific weapons, so there's no way to only apply the effects to turrets.
EMP Nova - Shouldn't be too hard. You might want to make sure the AI never uses this while the (allied) player ship is in range.
Retro Boosters - Cool idea. Writing proper AI for it might be tough as there's no way to ask vanilla AI when it wants to disengage. I think it's doable though.
Overload - Hey! I'm planning to make something similar 
Drone Launcher - Sounds like you want custom behavior for these drones. Could take some work depending on what you want and how picky you are.
Active Electronic Warfare - You might have trouble convincing the enemy AI not to ignore the drones with their main weapons.
Drone Bays - I don't think ships can launch more than one type of drone. Might be able to bypass this with hackery.
Phase Teleporter Cannon - Awesome 
Emergency Thrusters - Might be difficult to make the ship move correctly while the engines are offline. I can't think of any good, clean ways to do this.
Missile Factory - Shouldn't be too much trouble.
I believe most of my ideas have already been implemented in various mods, or I saw something approaching.
Precision gear: I don't need to apply this only to turrets since the ship only has turrets! (Am I clever...) And FlashFrozen already did exactly that with his Maul.
Drone Launcher: I'm pretty sure I saw that someone made a missile weapon that launches drones, so I don't worry much for this one.
Overlord:
It's the one I'm worry the most about, I hope it won't hit some hard coded stuff.Scratch that, I've been informed that the function already exist in Dev mode...
Active electronic warfare: A drone with the sprite of the ship should do the trick for the players. As for AI, if I flag the drone as a capital ship (or push up whatever the AI uses to judge the power of a ship) shouldn't it target it? I mean, can I launch a Capital ship from an other ship?
Drone bays: It's a bit early to promise anything but in fact I originally intended to make three declinations of each ships, scouting, warfare, and defense. Each one would have had his specific drone type.
Phase teleporter: Yeah, I almost build the whole faction just for this one!
Emergency thrusters: I doubt there is an easy way to do this. Maybe it will fire up automatically when your engines are shots? Giving you few seconds to generate an escape vector...
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