Ships almost always have much more shield and armor then hull points. This makes the sub-system damage function useless, as ships always get destroyed instantly when shield and armor is gone. To change this, the armor should increase hull points rather then give the hull extra protection, so that ships may suffer sub-system damage once shield is gone. Armor should provide more hull point then the armor point it used to provide, so that it can be as useful as it used to be. Weapon with AP trait should do slightly more damage to hull and have significently increased chance to destroy sub-system instead of penetrating armor.

What are you (unsuccessfully) trying to accomplish (in those battles)?