At the moment there are basically four uses for ships: combat, conquest, cargo, and colonization/construction. All of these are necessary, and all of them have corresponding modules. This is great, but even more could be even better. To wit:

Something that might be nice for an update or (more likely) an expansion would be more specialty modules for ships. I'm not talking about cloaking or anything like that; I'm thinking things like fleet speed boosters or diplomatic modules that would improve relations with other races. Clearly the former would have to be huge to keep them from being massively unbalancing (especially if you extended them to include low-level weapons boosting, too). You might also have something like an orbital bombardment module designed to support ground invasions (or even provide new invasion tactics) on planets it's in orbit around.

This would make cargo hulls even more useful, but it would also require more strategy to properly deploy and protect them. To prevent them from unbalancing, you could put a limit on bonus stacking (to differentiate them from starbase modules, say) and make them huge (e.g., =>40 units or so). Add to this the opportunity cost of having your shipyard build these instead of combat ships or constructors, and I think would add an interesting strategic depth to the game.