[Zanthis]

Well, a lot of this could be fixed by having components take partial damage. Then you could eliminate the extra damage system and things would work like you'd expect.

However, that requires every component track damage it has taken, which might be annoying to program. So, you could stop adding extra damage to each weapon's damage. Instead, add the weapon's damage (after shields) to the extra damage and use that to destroy components. Reordering how things are done in this way would go a long way toward helping things out.

In fact, the only thing that would not fix is organic armor, using armor-skipping weapons to sneak normal damage past armor, and having phased and non-phased shields at the same time.