I am also back off of vacation, and TS, I gave some thought while driving to your idea of having colonies be a bit simpler. I think the key ios to have every colony start with a colony hub, which would have a spaceport, some storage, and construction abilities, plus whatever bells and whistles you like. Evry colony would build that first, and then the "resource generating" modules. In my view, this would replace shipyards completely, at least for colonies. Level 3 CHs might even take on some of the attributes of the Military outPosts, with training capabilities.
The existing AI_Construction_facilities files would require only a minor tweak, which I could do (in fact, have done!
) Done right, this would allow players to just turn over their construction to the AI as the AI would be as efficient as the players.