Someone else posted a very good idea on this a while back. I don't remember all of it but basically the idea was instead of facilities per planet size, it was facilities per amount of population. Eg. after you grew or transported another 100 mil(or whatever the number was) in population, you could build another facilitiy. And then a planet had different pop limits based on whether or not the people had to live in domes.
At least I think that was it. Maybe I mangled that badly.
Geoschmo