I have been thinking about it for a while. I started with Brad's idea of a separate Shipyard and got inspired by some of the great ideas I read from you guys on this thread. I think I can suggest a pretty decent concept of how the Space ShipYard could work. Feel free to comment.
1. Planets Have a Starport that allows them to build Basic Small ships and cargo module ships using the regular planetary production queue. But those cannot build bigger war ships ( Moo2 anyone? )
2. At some point you build a constructor ship which will become a specialized Shipyard Starbase. The big capital ships can be built in these starbases only.
3. The Shipyard StarBase has a range of effect, like other starbases, and collects the Production from the planets in that range. Typically you would make one shipyard for the whole solar system. For example, Instead of having 3 planets each build a ship, you have one big starbase building 1 ship 3x faster.
-Let`s suppose this starbase is your new shipyard. It would collect the production from both Earth and Mars as they are in its range.
3.b Alternatively, the system could be made that planets are linked to the shipyards in the same way as asteroid mines are linked to the planets in galciv II. Penalties occurs the farther away the planet is. ( I kinda prefer this one honestly )
4. The amount of manufacturing that is allocated to the Shipyard by the planets is determined by a slider. It sets the percentage of total manufacturing that is allocated to Shipyards. This would work along with the production wheel and could be set both at Empire level or Micromanaged on a per world basis, Just like the wheel. See it like that: The planets build ship parts in factories and then the parts get sent by shuttles to the System Shipyard where they are assembled into SpaceShips.
5. The Shipyards Being Starbases have their own GalCiv III style dedicated screen where they have their own build queue and can also be optionally upgraded by using more constructors. Because they are important you could add modules to defend them or maybe gives your ships some perks, the possibilities are vast. ( i edited the text in the image to give idea)
6. Maybe those good ol StarPorts on the planets could be kept as a requirement to allow the channeling of the production to the ShipYard. After all, you would need them to shuttle the resources. Incidentally that would allow a way to keep using the +1 military adjacent bonuses you get from your colony layout Those +1 bonus could be used in many fun and creative ways as part of the synergy between the planetary starports and the System shipyard.
Some advantages of a system like this ( in my opinion )
1. Has all the benefits of the Dual queue of GalCiv II
2. Is insanely cool and immersive: Also would be quite innovative as far as Space 4x designs go.
3. Consolidate your ship building in fewer but more efficient production centers : Reduces the number of queues to manage and the number of rally points to update while keeping the same amount of production. Less micromanagement, more fun.
4. New strategic options for warfare. Shipyards become prime targets for attacks. Also make them interesting for defense as they tend to Agro attacks.
5. The most basic ships are still buildable from planets: That would prevent a cheesy ''Checkmate'' endgame if one gets his shipyard destroyed early. Would also free the early part of the game of the requirement to build constructors when all you might want to do is build a few scouts and colony ships.