Like the first one.
Oh, and I'm using an armor system very much like that. Here's how it works.
I really only want armor to effect mass drivers and missiles, so they have the "kinetic" damage type.
Each class of ships has additive armor. Corvettes take 2 off the damage, Frigates take 3 off, Destroyers take 4 off, and anything larger takes 5 off. This makes smaller mass drivers useless against larger ships, exponentially favoring larger calibres. Frigate armor will make a huge difference against smaller peashooters, but almost no difference against the 42cm mass driver. So smaller mass drivers have a higher DPS when you don't factor in armor, but are usless against larger ships.
I decided against changing Ion Cannons and Plasma bombs right now...after all, any change in how they work will screw over fighters or capships, so I don't want to touch them.
In addition, I turned off auto subsystem repair for fighters, and enabled hull repair and subsystem repair for frigates and larger. It's better that way.
I can send the bomber, although I want to do a bit of work on the wings first but otherwise the geometry is done. It's not mapped yet, though.