Destructible modules, or item durability. E.g. "full health", "light damage", "heavy damage", "broken". We could set items to perform less optimally at different stages of damage or even be totally inoperable if they get broken.

Set flags to allow which weapons can have a %chance of causing this damage. This also opens the possibility of repair modules that fix items instead of shield / armor. In other words, more variety.

Edit:
This can also create more perks for repair; right now we have shield repair rate and armor repair rate. This can add item repair rate.

Another idea, firmware + pilot slot. Firmwares for fighters as well, not just mothership. Nothing major of course but even modest improvements (5%-20%) can help.