One of the issues that I had even with GalCiv 2 and am finding it happening now again with GC3 is that while I love the ship designer to no end... it still takes a long time to effectively create designs because it is entirely mouse driven. Clicking to place a part and then having to manipulate a number of "dials" takes a bit of time and requires looking away from the point you are attempting to work on. This keeps it from being quick, easy, and fun.
I would like to suggest finding inspiration for improvement in an unlikely place: Kerbal Space Program. Their ship builder is extremely easy to use, for one very important reason: they have bounded the rotational axis controls for their parts to the WASD/QE keys. This makes it extremely intuitive to use and to be able to put parts precisely where you want them, arranged how you want them. There are also a couple of keys to toggle auto-symmetry and to cycle through rotational constraints.
The ship builder's UI is great as-is, and the layout of the screen is fine. The only thing missing to make this perfect would be to add these sorts of hotkeys to make it that much easier to use.