[Barnacle Bill]

Not sure I get the percentage thing on penetration/damage absorbtion. A layer of sheet metal from a car door will stop a much larger percentage of the total damage from a .25 auto pistol bullet than from a .50 cal machinegun bullet. In fact, it might completely stop the .25 and not measurably slow down the .50 cal.

It seems to me that a more realistic model is to rate waepons for penetration and shields/armor for penetration resistance, with the damage actually taken by the target = D * (P-R)/P where
D = base damage caused by the weapon at the given range
P = penetration of the weapon at that range
R = resistance of the shield/armor

You could then have different damage types for which a given weapon might have different D & P and a given shield/armor might have a different R.

To prevent just piling on too many layers of shield/armor (so as to outclass all weapon P values), though, you'd want to limit the number of slots available for defenses but have something conceptually similar to mounts for them so bigger ships can mount a stouter defense.