Shipyard Planets not being able to have Mines.
This idea came from Ent, actually.. A shipyard planet should consist of alot of farms, alot of domes, and alot of Gens. The shipyard planet should rely on the other planets in the system to produce the minerals needed for ship production, and possibly factories, depos, and defence bases.

Barren Planets = Resource Planets

Thinking over all the Sci-fi I've seen, Terran planets have always been the nice comfy places. Where there isnt alot of industrial work going on there. The barren planets had all the mineral mines, all the blue collar workers.
Make it to where Barren planets can produce alot of minerals.

Depots and Defense Bases costing Resources

It should take abit of resources to repair a ship, yeah? While it might not be a large ammount, it should still cost something for the planet. And launching hordes of fighters, missles, and torps from defense bases should also be another drain on resources from the planets. It'd be abit more logical then the planet being able to throw hordes of defence and repairs without any sort of limit.

Limit Resources on a planet

A planet doesnt have infinite storage place for resources. There should be some sort of limit. This'll come into play with the next idea.

When an enemy ship is within a distance of a planet, all resources going in should be stopped. But the planet can still produce resources and spawn ships

This in a true sense is what a siege is. The population on the planet can still produce things, can still spawn ships. It just can't get resources in.
This would give the allied fleet a chance to spawn from the Shipyard to defend.