I think Bridge Modules would be an ideal way to customize your ships. Personally, i would like to see a customization system for bridges similar to the External Design system from Starship Creator.
Where you have like 100 of each component to choose from and purchase, to create a truly unique system. Imagine being able to customise the floor, the ceiling, the walls, the bridge layout, the consoles you have. It would be awesome.
I like this idea as Gorn aren't too big on science and medical heh.