1) starbases could be built in orbit around a planet or star. maybe have the modules only benefit that planet/star system only, but have them give a higher bonus.
2) ships should only be allowed to upgrade in orbit of a planet with a ship yard, or in a starbase, docked with the starbase (maybe a new module) and upgrades would be slower, using maintense funds, or a 1 turn upgrade with money. a benefit would be that the ships inside would help defend the starbase in an attack.
3) have a new module for ships, that allow them to carry tiny(large and huge) and small(huge only) ships. there would be a 6 and 12 logistics sizes, and ships inside would only count half their logistics. This could make some new ground invasion tactics.
All comments welcome.