[Suicide Junkie]

You can give weapons varying penetration levels in a variety of ways.

It is harder to give varying armor/shield resistance levels, though.

First:
If you have a ship with extremely high crystalline ability, the following will happen:
Skips Shields/Ships armor: 100% penetration.
Quad 2 shields: 80% penetration.
Double to shields: 66% penetration.
Normal: 50% penetration.
Half to shields: 33% penetration.
quarter to shields: 20% penetration.

Second:
If you have a ship with limited/varying crystalline ability;
If hull damage each shot < crytalline ability amount: use the above numbers.
If hull damage each shot > crystalline ability amount:
Quad: 1/4 of crystalline ability amount is absorbed, the rest penetrates.
Double: 1/2 of crystalline ability amount is absorbed.
Normal: ability amount = damage absorbed.
Half: 2x ability amount = damage absorbed.
Quarter: 4x ability amount = damage absorbed.

So if a ship has too little armor, the penetration goes up, but once the armor is a certain thickness, any extra plating is redundant.