I already proposed a system like this several moths ago - except I used the SPECIAL system instead the d20 for grabbing ideas, here is the big thing:
Multistage Developed - Improoved Damage SimulationStage I - Improoved Damage FormulaeDamage Treshold / Damage Resistance - Damage calculation system
A basic overhaul of the current damage system and instead the exiting - and somewhat hackish- flag system.
It will use a separate armor.tbl which either contains a variety of armors or is an addenda to ships.tbl.
Damage calculation is now: (Weapon Damage - Armor Treshold)*(100% - Armor Resistance(%))
The treshold simulates the deflection power of the armor - this will put an end to all the HUGE, BIG SHIP and ect. flag frenzy that never seemed to offer a perfect solution.
Armor Resistance is not really necessary at this point since you can simply assign higher hit points to bigger capships, but if you wish you can already simulate hevier armor plating and stuff like that.
Stage II - Armor Strengh SimulationPenetrating Damage = (WeaponDamage - Damage Treshold*ArmorHp(%)) (100% - Damage Resistance(%)*ArmorHp(%))
Armor Damage = (WeaponDamage - Damage Treshold * ArmorHp(%))*Damage Resistance(%) / Armor Endurance
Penetrating Damage = the old damage value aplied to the ship as usual
Armor HP = pretty self explanatory - the status of the armor
Armor Damage = this will be substracted from the ArmorHp
Armor Endurace - think of it as the armor resistance to falling apart. It simulates that even if the armor takes damage (absorbing it) it's stucture is less deformed than the interior of a ship, since the armor was designed to do so.
This advanced model introduces the wear of the armor - so the ammount of damage will gradually increase. That way a tiny fighter will be able to deal the last shot to a destroyer if the bombers already ravaged it with their heavy bombs.
This is the point where armor resistance becomes necessary - it actually simulates the ammount of damage the armor absorbs when a shot goes through it.
Stage III - Localised Armor StatsSelf Explanatory title - segments of the ship have their own armor simulation - prelude to true armor plate simulation
Stage IV - Segmented Damage ModelOnce Segments are defined in Stage III - they can be used for simulating damage to individual parts of a warship.
Stage IV-2 - Complex Segmented Damage modelSegments have key components(subsystems) that dictate the segments performance.
Stage V - True Surface Damage SimulationDevelopment of true armorplate simulation on the surface of the ship.
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Stage VI-A - True Geometric Armor Plate SimulationArmor plates have a thickness - may be impossible due computing needs
They take damage accordingly
Stage VI-B - True Geometric Damage ModelShip sections take damage based on the penetration of projectiles into the ship's interior.
Requires advanced ship parts with varied components - uses the already suggested Reliability/Performance/Repair system with key/secondary systems in a subsystem or a ship section.
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BTW someone even coded smg. like this
http://www.hard-light.net/forums/index.php/topic,17366.0.html