I have thought about this a bit, but why don't factions have some basic defense guns on their factories and such? I would expect a factory to have a measly little peashooter to attack fighter craft, since they are valuable structures. Yeah.
Also, every space game that I HAVE PLAYED had the typical system of ship destruction: You shoot, the ship explodes in a spectacular fireball. But, what if a ship was shot up, and virtually destroyed, but it did not explode, say if the crew managed to turn off the power source or something. Maybe ships, when destroyed, could have a chance of simply becoming derelicts that can be salvaged by construction vessels.
My two bits...