I don't think there is a way around this, but I thought I'd ask everyone how they handle this. Let's assume that you have researched "Applied Research" far enough to be able to build Research Center III's. With default construction rates for a planet without a spaceyard (2000 M, 2000 O, 2000 R), I like to build Research Center II's until the planet is full and then upgrade to level III's because II's can be built in 1 turn, but III's take 2 turns to build. Let's leave other variables out of this discussion for now like Central Computer Complexes and System Computer Complexes and using spaceyards everywhere. I use the same scheme with mineral miners, intel centers, etc.
Here's the part that bugs me.
Once I get level III of any of the facilities, upgrading facilities has to be done on a per-planet basis. I can no longer use the Construction Queues screen to "upgrade facilities" because it will switch all my level II facilities in various construction queues to level III's. What I really want to do is only upgrade those planets which are already full. I actually dread getting my first level III facility of any kind because of this, and that level III facilities aren't that much better than level II's.
So here's the question: how do you guys handle this?
Slick.