I've got an idea for Starsector!
I'd like to propose a shield generator/projector subsystem on ships, almost exactly like engines and weapon hardpoints. The shield generator would be disruptable just the same as engines and hardpoints are when taking damage/EMP. Maybe it's possible with direct damage from weapons fire as engines and hardpoints are, but maybe the shield generator is only disruptable with EMP damage, EMP arcs, and/or large radius, heavy damage explosions (the idea being that it is tucked away safely inside/away from the edges of the ship). Perhaps beam and kinetic weapons are not able to penetrate through the armor/hull to hit the shield generator at all, or maybe most or all weapons can disable once there is no armor left between the point/angle of weapon impact and the shield generator within the hull. I'm not sure how vanilla does it for turret hardpoints, in terms of being disabled by weapons fire as it eats through the hull. Maybe this is all set in the combat/damage system perfectly already and the shield generator can work the same way, though perhaps less or more fragile.
Next, and perhaps separately, I propose flux overload from shield damage only deactivate the shield and ship special (high energy focus, burn drive, etc). While flux overload is in effect weapons can be used, however they have a chance of malfunctioning in a similar fashion to low CR malfunctions. In this case malfunction chance would depend on the flux generation of the firing weapon and/or the total flux of the ship. Higher flux-per-shot weapons (gauss cannon, plasma cannon, antimatter blaster, etc) will have a higher chance of malfunctioning as they fire, the idea being that it is a larger strain on the flux system of the ship. Weapons with lower and more steady flux generation (beam weapons, for instance) will have a lower chance and/or take longer to malfunction. This weapon malfunction might be calculated as if the weapon was causing "flux damage" to itself. For example, a ballistic weapon that generates 500 flux for each shot might cause 250 "flux damage" to itself for each shot (damage number not shown in game). For simplicity this "flux damage" might simply be calculated as if it were actual EMP damage for the purposes of causing the weapon malfunction. The total flux of the ship may function as a threshold or multiplier of sorts when determining if a weapon will malfunction due to "flux damage". Or, simply taking the flux generation of a weapon as a percentage of the total flux cap of the ship would be a good route for determining weapon malfunction chances. As for beams, I'm thinking a build of "flux damage" will accumulate as long as the weapon is firing, eventually malfunctioning for certain. Probably faster/easier with higher current flux, just as non-beam weapons.
Like weapons, during a flux overload engines may be used almost as normal. Risks could be an automatic percentage(?) decrease in thrust, a chance for part or all of the engine to malfunction when thrust is activated (similar to current vanilla behavior when engines are partially damaged but not fully disabled), and/or being more sensitive to damage/disablement from weapons fire.
Hull mods like Resistant Flux Conduits and Insulated Engine Assembly (or new ones, like "Surge Protectors") could increase the resistance of weapons and engines against these malfunctions.
Other than the details regarding weapons and engines talked about above, flux overloads caused by shields receiving too much damage would function just as in vanilla, eventually dissipating and returning to normal. A shield generator disabled by EMP arc/damage or weapons fire would eventually be repaired just as engines and weapon hardpoints are disabled and then repaired in vanilla.
The flux overload animation could be changed so that the light purple electricity crawl originates from the shield generator/projector, in a simialar fashion to how EMP arcs originate from the EMP weapon impact spot when jumping across to other parts of the affected ship. The purpose of this is mostly to highlight the location of the shield generator, both for fun and combat tactics, like highlighting a weak spot. It would also be pretty cool if, when a weapon or the engines malfunction due to use during flux overload, a larger purple arc shot off from the shield generator and into malfunctioining weapon/engine. The same as EMP arcs really, but not coming from an EMP weapon impact and a different color so it is distinguisable to the player.
I think this would add some fun depth to both the gameplay and the immersion in combat. I already see where the shield generators (yes, sometimes multiple!) could be on the Paragon. Those two semi-circle blue doo-dads down by the engines, nestled up next to the turret hardpoints. Though, maybe they'd need to be moved up just a bit to be easier to hit through the armor on their respective sides. Also, probably for simplicity, disabling one would disbale both.
YAY STARSECTOR, YAY SPACESHIPS!!!
TL;DR - Shield subsystem that can be damaged (like engines/weapon hardpoints). Flux overload doesnt disable weapons, but risk of malfunction when firing during flux overload. Hull mods could reduce malfunction chance. Don't be lazy, read the whole thing.