Some bugs and suggestions:
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Starbases stealing constructors. It is possible for multiple starbases directly ordering constructors to get fewer constructors than what was ordered and for other starbases to get more than what was ordered. I call this constructor stealing. After many tests, what seems to happen is the shipyard will give the flight plan of next constructor to be built to the constructor that was just built. If a constructor is the last item in the build queue, then things work as they should. So if you order 4 constructors to one starbase and then another 4 to another starbase, the first starbase will get 3 constructors because 4th got the flight plan of the 5th constructor. So the end result is the first starbase gets 3 constructors (4-1) while the second gets 5 constructors (4+1).
To examine this problem a little bit further, if you had a ship (maybe a scout or another constructor) in front of the first constructor ordered, it will get the flight plan of the first ordered constructor. So a single starbase would wind up with an extra ship when everything is said and done. Likewise, if a ship is placed at the end of the queue, then the ship in front of it will adopt the flight plan of the ship that comes after it. So a single starbase would be short of a constructor.
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While the fact that we can now directly order constructors from starbases, some people have pointed out that you can only order the normal constructors. Basically you are forced to use whatever constructor the game designs for you instead of using whatever model you have designed for the job. Your design ships could be a constructor ship stripped down of everything that is not the hull or constructor module, or it could even be something with multiple constructor modules. Regardless of how well you have designed it, the starbases can't be made to order it. Of course, if your techs improve to the point where you get more expensive parts and more miniaturization, then the normal constructors will get more expensive and hence slow things down.
The only way to avoid this problem (at this time) is to opt out of using the constructor ordering mechanism from the starbase and upgrade your starbase like you could in beta 4.
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Something that has came up when I was using order constructors (a lot of it) is, it is difficult to judge how many constructors you will need to fully upgrade a starbase, or just upgrade select modules. The problem is that not all modules are revealed at once. Many modules are unlocked once you spend a constructor point to install the prerequisite. Unless you taken the time to count up exactly how many constructor points you need for the configuration you want, you are stuck guessing how many constructors you will need to order.
There are a few ways to fix this. First off, you could make it possible to see all modules that can be unlocked by installing a specific module. For instance, if I look at the economic starbase upgrade, I would like to be able to tell that I could get 3 manufacturing upgrades and 2 morale upgrades. I could then decide that I need to order 5 constructors. Alternatively (or to complement other options), we could get the tools to tell the starbase how to upgrade itself and allow it to order constructors as needed. For instance, it could be told to automatically upgrade all manufacturing and morale modules when possible.
GalCiv 2 had the ability to automatically upgrade starbases if they got constructors. I something like that or better would be nice to have.