One issue I find is managing my atmosphere.
Maybe there could be an advance atmospheric scrubber where it turns on when the atmospheric pressure hits a value that the player can set. That way, we dont have to worry about managing atmosphere. It can use up resources like software and water to keep the electronics of the building running.
Another thing that I think would be cool is adding nuclear waste as a material. Reactors can produce this after using up uranium, and the uranium refineries can be used to convert the waste back into useful product.
Another idea is a fusion reactor. It can produce lots of energy from using helium 3 as fuel and lots of water for cooling. It can produce small amounts of uranium, gold and aluminium as a byproduct of the fusion process, but to balance it out, it can be a very big building and also use up microchips and robots due to the reactor needing to be serviced a lot. It could be upgraded so that it incorporates alien technology to create a something like an artificial small star reactor that uses less materials to run, but needs ancient instructions, nanites and artifacts.
And my final idea is cyborgs. There can be a building which can convert people into cyborgs, meaning that they no longer need food, water and do not age, however, they now need lots of power to keep them alive.