I think something that could spice up the gameplay and expand new ship design/customization possibilities would be gun ports on ships. Essentially, a particular set of guns on a given ship would be protected by the armor and hull (closed ports) until someone mounts any of said guns (opened ports). This would prevent your ship from being completely disarmed from a distance and allow engineers to focus on more defensive repairs (hull, balloon, engines) while you close the distance. This would also translate into not losing your guns the instant you rebuild them, thus allowing you to fully repair them before using them again. The catch is that it would take an amount of time for the gun port to open, so you couldn't just immediately open fire once you mount the gun.
I've got some expansion to this (different ways it could be implemented and stuff) but I wanted to just throw this out here first before making some long-winded, be-all-end-all post.
