Mystikmind, your tip does not solve the problem at all. You still have to manually search the map for flaged starbases and decide what to do with them.
I think the best solution would be an option at the starbase that unusable constructors should be ejected and maybe even send to some other target. If they are ejected they will show up as idle anyway. If they could be send to some other target, you could collect them somewhere.
Of course the coolest thing would be if the game would be so smart to use the left over constructor modules for upgrading other starbases.
In the final stages of my current game I get 16 constructions points on one constructor. Now of course it is more efficient to build the 16 points constructors than 16 constructors with one point - so of course the 16 pointer is the default for the starbases. But what happens if an starbases only needs 1 point for upgrading some module? You guessed it! I have 15 constructions points sitting at hundreds of starbases ... and all I can do is manually move around the map to make use of this hidden treasure.
All in all, the starbase building is better now but it still has some quirks. Aside from the above it also lacks the feature of the building plans that GalCiv 2 had in the latest edition. It still requires a lot of tedious clicking, especially if you have a fleet of constructors with enoug modules ton build an entire fully stocked starbase in one go - you have to click for all modules and their upgrades. GalCiv2 had this solved way more efficient without giving up the control.