About the AI colonies: is the AI capable of making domed colonies undomed if it has the right population? If transporting the non-breathers of the planet is too complicated you could just let the AI 'scrap' the offending population
. It would give them tons of extra facility space.
I was quite suprised to see that you can scrap populations without any obvious impact on loyalty or happines, perhaps that should be considered a SEV bug though. The whole domed-undomed thing seems quite awkward, It would make far more sense if a planet became undomed if a population is present that can breath it's atmosphere, even if races that can't breath it are still on the planet. The non- breathers would stay domed, and would be limited in their growth by the maximum domed capacity, but I see no logical reason why the race that can breath the atmosphere couldn't populate the rest of the surface. That's more of an SEV issue though. I'm looking forward to the patch.