I'm not really sure if it's possible, but I think adding a ventilation system fro the base would add a bit of depth to the base building so you'll actually have to design it well.
A pro of this idea is that it means you can have one big life support room, so your technicians don't have to wander around the base being negligent of all of the vital system. It also means that making death-rooms for dangerous crew members and raiders is easier. Your bases will have to have some thought put into them to ensure that oxygen gets into rooms. Rooms with closed doors should be effectively air tight, seeing as it's in space, the same way submarine doors are all water tight.
If disease is ever implemented, you would have to build a closed life-support system for all the ill crew, or risk infecting your entire crew. I think this would be pretty fun, along with other disasters, such as meteorites cutting open the ventilation pipes and leaking your precious oxygen into space, and would make the game far more exciting.
I know this is a proof of concept, but I was thinking that the ventilation could be on a different plane to the main base, similar to SimCity 4, where you need to control the water supply underground through pump stations.
Tell me what you think, it's just an early idea, but it's something I would really enjoy having in the game.