First let me say, I hate constructor spam. I'm not big on micro and I see this as a lot of micro, over and over and it makes me choose basically between infrastructure and capability.
My issue here is that this is one of the places GalCiv needs to improve and while if I remember correctly Paul made a comment on one of the dev streams about and improvement to how starbases worked but I don't believe he said what it was. So here is my suggestion, treat starbase modules like buildings. When an update becomes available the starbase starts building the next step in the chain like the the basic factory automatically updating to the xeno factory, the worlds in the starbase's area of effect contribute production to do build it, say 10% or it becomes an update in one or all of the worlds build queues. For starbases that do not have worlds in their area of effect to support them buy the modules, I would thing very few people would object to just paying upgrade their archaeological or mining starbases or tie them to a sponsor.
This allows at slower speeds to build your infrastructure and your capability at the same time, removes the annoying micro of sending constructors to all your starbases every time you unlock an upgrade and makes late game starbase construction much easier. Additionally this might allow military starbases to remain useful later in the game. Edit: I think I meant to add buying modules would allow for faster builds as well but got distracted.