I've recently got an idea inspired by realistic flight sims and Wing Commander. FSO subsystems are rather limited in what they control, not to mention they generally work on an on-off basis. I'd like to see more subsystems available to modders, with dynamic damage effects. For example, if engines are down to 50%, so is your max speed and acceleration. In order not to break retail, I thought off a few new names for them, grouped into "sub-subsystem" categories. Not all of them would have to be on every ship, if the subsystem is absent, the "master" would control it's function. In POF and table, they'd all be normal subsystems, I only grouped them for ease of reading.
The list I've come up with:
$Engines (retail)
-$Thrusters (thrust and acceleration)
--$Forward, etc. (thrust and acceleration in the given direction, either direction or "Vertical", "Horizontal", "MainAxis")
-$Controls (maneuverability)
--$Pitch, etc. (maneuverability in different directions, it'd be a "sub-sub subsystem")
-$Afterburner (AB speed, charge and recharge speed)
--$ABCapacitor (AB max charge and recharge speed, if no generator is present)
--$ABGenerator (AB recharge speed)
-$Assistance (destruction forces the ship into glide. I don't think it'd be used often.)
-$Generator (master recharge control for all systems that don't have their own generator)
-$Capacitor (master capacitor)
$Weapons (retail)
-gun1b1, etc. (gun or missile points in a bank. This would work like damaging weapons subsystem, but only for a single gun/missile Also affects external models)
-ammopb1, etc. (health directly translates to ammo in a primary or secondary bank)
-$WepCapacitor (Weapon max charge and recharge speed)
--$WepGenerator (Weapon recharge speed)
-$Autoaim (controls autoaim FOV and how tightly the autoconvergence converges)
-$Countermeasures (CM dispenser)
$Sensors (retail)
-$RWR (with damage, missile warning become inaccurate and mess up)
-$IFF (everything is shown gray on the radar when destroyed)
-$Radar (disables the radar)
-$FTLScanner (subspace arrivals aren't shown on radar)
-$Targeting (disables targeting)
--$Locking (disables missile locking)
-$Stealth (disables stealth)
$Communications (retail)
-$FTLComm (disables calling for things that warp in, if the support ship/reinforcements arrive from a ship in mission, they'd be unaffected)
-$RadioComm (disables everything except the above)
$Navigation (retail)
-$Autopilot (disables AP)
$Shields (new big subsystem, controls shielding on an on-off basis)
-$FrShieldCapacitor, etc. (max shield quadrant integrity and recharge. Without quadrant identifier, it applies to all otherwise uncontrolled quadrants)
--$FrShieldGenerator, etc. (shield recharge, can also go without a quadrant identifier to apply to the whole ship)
$Cockpit (destruction doesn't kill the pilot, but scrambles the instruments)
-$HUDradar, etc. (in general, $HUD[gauge name]. Destruction disables a specific gauge. Very situational, or for modders with OCD/Hyperrealism obession (yes, I'd use it

))
$SelfRepair (controls self repair)
-$RepHull (hull repair)
-$RepSub (subsystem repair)
-$RepSupp (subsystem for a support ship, affects it's repair speed of other ships)
$Turret##
-$TurretGen## (disables the turret when destroyed)
-$TurretSens## (affects the turret's accuracy)
-$TurretAmmo## (health directly corresponds to turret's ammo load, if that's implemented)
-$TurretServo## (on multiparts, controls rotational speed)
Now, I'm aware it's a huge idea, probably a lot of coding, and not all those subsystems would be useful to everybody. I don't know how much of this can be done with scripts, but I don't think all of it can. I think that some of more realistic mods could use this kind of extended subsystem set. It'd bring it to par with most flightsims, Starshatter and Wing Commander on this field. Some suggestions might seem outlandish, but I've posted everything I've thought off, without thinking of feasibility, since I'm not requesting anything, just throwing an idea.
EDIT: Added a couple of ideas for turret additions. They'd probably be very situational, but could still be useful.