I agree with Tobi-wan_Kenobi. Make it shoot everything, but focus, primarily, on missiles. Hell, make missiles an entity that can be shot by anything, even your Ion Blaster. Thing is, it would cost very little energy to shoot, and it would deal little to no damage, but the missiles would have a VERY low HP. It makes sense.
And that auto-fill storage thingy. It's pretty much "merge adjacent storage". so that they wouldn't have to travel to the other room when the storage room closer to the gun/whatever is empty. it's really anoying when you have a lot of guns. Even though it forces you to think about your ship design... it's annoying, because it's ridiculous. We're fighting in space, it's ridiculous enough that the crew has to carry energy cells instead of the reactor just being plugged into an energy network, but that's game mechanics, i guess. At least make it less ridiculous, it's all i'm saying.