Combat System Overhaul
I would like to see a combat system overhaul. The current mechanics for the acquisition and destruction of components on board ships is a little too simple. Targeting everything with computers can create some issues especially if the goal of the offense is to capture the ship to re purpose and/or refit it.
Make ships use antennas that can detect computers through some sort of wireless signal ( however you can work it into the lore).
Add more options for targeting specific blocks on ships first ( priority: ie target weapons before anything else)
More weapon choices, Mods currently do an amazing job of this but it would be nice to see more in vanilla that aren't as bulky as a 3x3x3 simple turret. Heavier artillery/cannons would be nice to have as well.
This can also tie into my earlier post about giving beacons a purpose.