Just saying, I dislike percentage armor. Half inch thick armor plate will go a long ways towards making you immune to 0.30-cal rifles, but it's not going to do anything significant against 15" naval cannon. Percentage armor says that your armor plate has the same magnitude effect on both, and I simply don't feel that that is reasonable. Armor should have the most effect on the lightest attacks, and that doesn't work out to 25% less damage from all sources. Moreover, the proposed X% armor penetration, where you'd reduce the Y% armor to (Y - X)% armor also works out strangely. I don't care if you put armor penetrating bullets in your 0.30-cal rifles, they aren't that likely to do that much better against my half-inch armor plate than the non-armor piercing bullets are, and the 15" naval shells would have blown through in any case. Neither one should work out to a (X + 100 - Y)/(100 - Y) damage bonus in the general case (yes, for specific levels of armor against certain strength attacks, it could be reasonable, but not for all powers of attack against a specific level of defense).
@Tridus: giving the Armored Golem 80% Armor in a percentage system is very different from the current system, under the proposed armor-penetration model, unless you happen to be talking about the things which have significant amounts of armor penetration. It boosts the Armored Golem's durability against anything that deals more than 125,000 damage per shot, because the 100,000 armor of the Armored Golem only applies as an 80% reduction to anything under that (which, granted, is most stuff), and an armor penetration which reduces the armor to 75% instead of 80% is probably not the same as armor penetration which reduces the armor from 100,000 to 95,000. Going from 80% armor to 75% armor represents a 25% damage increase for anything with that 5% armor penetration. Going from 100,000 armor to 95,000 armor in the current system is nothing of the sort against most ships; for that matter, going from 100,000 armor to 95,000 armor in the current system only makes a difference for those ships with more than 118,750 damage per shot, as anything below that is still going to suffer an 80% damage reduction against 95,000 armor, same as it would against 100,000 armor, which makes the armor penetration a 0% bonus for sufficiently weak weapons, and of varied significance for more powerful weapons. Something with exactly 125,000 damage per shot? 5000 armor penetration gives you a 20% damage bonus. Effective damage bonus forms a curve maximized at the point where you'd have 80% damage reduction from armor for no armor penetration.
It is unreasonable to me that a ship armed with light armor-penetrating weapons should gain as much from its armor penetration as a ship armed with heavy armor-penetrating weapons given that the armor-penetration value is the same.