I didn't read most of this as I am looking to sleep soon but I wanted to post something. I know it may have been mentioned already.
An idea for something to look at for this would be to have it be more efficient to have bases dedicated to certain things. For example certain buildings can synergise with other ones. Having airplane manufacturing right beside related facilities like a hangar could give bonuses to construction speed and reduce cost. However you could also have a weapons storage building beside the hangar too which could speed up rearming your active aircraft.
The idea could be that you could build a base that could be very efficient at 1-2 things but not everything. However there would also be nothing stopping you from building a base that can do everything adequately.
The one potential I could see with that though is having resource management get tedious. Having a global pool of resources, while not very realistic, would get rid of what I think might be a micromanagement wall of tedium.