First, why is using our Shipyards for building military ships and the occasional colony/freighter a BAD thing? Do we really care what our shipyards are doing per-se? All we care about is effect no?
What I do understand is that they want Starbases to COST you the time/energy/material that could be used on military ships, but there are cleaner ways to do it.
1) As I mentioned in another thread, make Starbases require a planet sponsor to produce, thus stealing production from yards/military ships.
2) Alternatively, you could add a third slider to the Govern production sliders, you can have Social/Military/Starbases
I prefer #1, but #2 is essentially the same thing, but lets you steal that production from the social projects instead of the military, which is why I prefer #1. I don't think we or Brad should care HOW we steal production from those shipyards, at least not when we are saying "This isn't fun and I need to be doing less of it" and changing things would help.
If building non-military ships from yards is really the goal, I can think of several ways to help with that.
1) Make trade routes multi-ship-able, so we build frieghters more.
2) Make the survey tech MUCH earlier, so we have a reason to build multiple Survey vessels.
3) Mining Ships instead of mining Starbases.
4) Espionage Ships which work just like Freighters, build them, send them to planet, they give you a vision bonus and some more details on the empire. Enough ships and maybe you start leeching credits? Diplomacy penalty is a result of course.
I don't actually LIKE any of those ideas (well, except the survey one), but they accomplish the task of "not just military ships" without being AS repetitive as the constructor mini game.