Some ideas.
1. Starbases.
The automatic sponsor assignation takes the nearest shipyard and the last built shipyard as the 2 default sponsors of a starbase. I think it would be better to take only the nearest shipyard, and to let the user add the other sponsors. With the actual system, I have to systematicly remove the last built shipyard from the list of sponsors of the newly created starbases.
Another idea is to give the player the possibility to remove an installed module from the starbase, usefull in case of error, or when some modules aren't usefull anymore like the research modules when the research tree is all completed. So removing these modules would save some money.
2. Shipyards.
My first idea is that each shipyard could have a primary and a secondary production. Each turn, the manufacturing points going in priority to the primary production, and the remaining points going to the secondary production. By this way, a shipyard could produce a maximum of two ships a turn, and some production will be saved when building some small ships. When requesting a constructor from a starbase, it would be queued in the primary production list.
In the Shipyard User Interface, the user could click the tab "Primary" or "Secondary", on the top of the ship production list.
Another way, but probably more complex to implement, could be to allow a planet to sponsor many shipyards. It would need to well distribute the manufacturing points between shipyards in order to minimize the number of turns to produce the ships. An alternative could be to allow each planet to have a primary and a secondary shipyard, the manufacturing points being sent in priority to the primary shipyard, and the remaining points sent to the secondary shipyard.