I think this is also the best solution; just a new system to augment the way it is currently, not a complete replacement.

Which is actually what i suggested. In my thread.

The problem that I see that keep coming up is that nothing in this game should be destroyed completely. If one class, for whatever reason has its main source of damage able to be blown up, then all eight should either be this way, or none at all. No need to single out the black sheep in a field of sheep of all colors of the rainbow.

I'm also for fighter hangars and mobile missile foundries, but drone generators are what I suggest now, and as the only thing that exists.

Make drones take damage, just as everything else does...

If a drone is destroyed a damaged version will spawn in your ship again (just as in the Colosseum), this damaged version will have a % reduction in stats that increases each time the drone is damaged. There may be a new item to 'warp' these drones before the moment of destruction, up to someone or other...

And if that won't work implement this along with drone generators, except instead of generating drones these slowly repair drones (for a small fee) as opposed to the instant repair of AI bases.

Either way drones should require time to repair and should not be spammed during combat. With a system like this people would still want to protect their drones. A because of eventual repair costs and (B) because they are rendered weaker and thus less useful after each death in combat.