[Alneyan]

You seem to have forgotten the Stealth and Scattering armour for the Crystalline ship. Or does it fall under the essentials? Likewise, you could put some Armour III on the Crystalline vessel, to draw more shots to the non-Crystalline armour (or simply put more Crystalline Armour, and remove one or two shields).

Ah, you weren't asking for a better Crystalline design? I have to agree with you; the Crystalline armour is more powerful than virtually anything else, costs being equal. The Talisman is, of course, the exception. A swarm of fighters could also work well, if you launch them in big stacks; they are treated as a single weapon, and will wreak havoc on the Crystalline armour.

That aside, the most common design is Shield Depleter/APB/Shield Depleter/APB and so on. This works quite well, but requires you to score hits fairly often, to avoid breaking the sequence. And this design is only useful against the Crystalline armour special effect, still leaving a pretty good defence on the target ship. The other easy solution would be to go with heavier weapons, such as the Enveloping Acide Globul (very expensive to research, and Organic only, but with a higher damage ratio AND a faster reload rate than the WMG). Again, having good odds to hit is more or less required.

So I feel you will need to put more ships and/or more expensive designs to take care of a Crystalline fleet. That, or simply kill them early on, and/or use the Equalizers (happiness and Stellar Manipulation). I know I have failed to come up with a working design to nullify the Crystalline Armour, without being at a disadvantage.