I'd apply decent copper plating for protection instead of going with a light-armor design. It should be capable of taking multiple hits and continuing to fly. I want to build something solidly reliable. Basically, all we're designing now is the hull, so after the following conjecture I'm going to propose a similar plan:
In fact, we may want to experiment with some form of steel "shielding", as in a last-ditch-defense layer made of steel, protected by the copper or bronze primary armor. Anywhere that an aetheric weapon burns through the weaker copper or bronze plating, it will reach steel, which will certainly last to the end of the battle. If it can't be patched, the steel will rust in the area exposed to the air, but the ship will have been saved and can be repaired.
To that end, let's try something easy yet adaptable like this:
Windrider class Frigate
This simple hull is much larger than the Skyskiff, roughly equal to the Transport Barge in length, though it is substantially thinner and lighter, as it has no need for cargo capacity. The hull is made entirely of wood, with a basic copper "skin" to prevent total failure in the event of a single aetheric cannon hit. The real genius, however, lies in its adaptability. It has 8 mountings for weapons, three per side, one fore and one aft, internal space left open for all the crystals in any configuration that you could ever want, and its armor plates are notched, allowing additional copper or bronze armor plates to be mounted directly to the ship with ease, or for them to be removed or replaced even easier.
I won't speculate on the projected costs, but this ship will be capable of taking any upgrades and adaptations we throw its way, without being terribly difficult. This should give us a designing advantage, as we just call in one or two of these hulls for refits whenever something new is deployed.
Draignean, what does a dockyard capable of running a production line for Transport Barges look like? How about one capable of producing the above frigate?