I recently had a good idea for my Star Trek game, this would also solve the problem with some factions having very few ships designs, and might even allow me to add more factions (Ferengi, Dominion, Kazon, borg?), seeing that finding and balancing enough ship classes for each faction was the biggest problem with adding more factions.

It might even make it possible to add some more exotic factions (Xindi, Gorn, Breen, Son’a, Tholian, Vidiian, Hirogen, Tzenkethi or maybe even the Terran Empire

Instead of just having 4-5 static ship classes where all ships made of this class are identical, one could have a little star ship designer where you fit a hull with the components you want (warp drive, impulse drive, phasers, torpedo launchers, sensors, fusion reactors, shield emitters, armor, cloaking devices, troop transports, colonization and terraforming tools).

This means I will have to do some re-designing the next time I have time to work on the game (wont be that much, only implemented 2 ship classes so far)

According to my superior mspaint skills, the interface will look like this: