[Suicide Junkie]

But then you have the RL shields, which work differently by blocking SOME shots and letting others pass through unharmed. Sigh.

I suggest the leaky shield system.

What you do is:
1) Drop shield generation amounts as nessesary (eg: 1/10th to 1/40th for standard SE4)
2) Add a "shield generation from damage" ability (the crystalline armor ability), and set it equal to the shield generated.

This means the shields will block half the damage coming in instead of 100% or none. They will also keep protecting your ship until the generator is hit.

By using the "X damage to shields" abilities, you can have various weapons penetrate more or less than others.

Quarter damage to shields = 80% absorbed, 20% penetrates.
Half damage to shields = 67% absorbed, 33% penetrates.
Normal = 50% absorbed
Double damage to shields = 33% absorbed
Quad damage to shields = 20% absorbed
Skips all shields = 0% absorbed.