Something which I've liked the idea of since seeing it partially in Spacechem is nested systems, the same concept is in Factorio with the Factorissimo mod.
The interesting thing about these subsystems is that with the right tweaks they can be blackboxed, for those who don't know what that means wikipedia has this "...when a machine runs efficiently, when a matter of fact is settled, one need focus only on its inputs and outputs and not on its internal complexity".
In other words you could take a Factorissimo factory, simulate it for a few minutes and say "Ok, as long as the inputs remain constant at X then this factory can produce Y units per minute". Once you leave the factory then that's all that needs to be simulated, as long as the raw materials keep coming at the set rate then you don't need to worry about simulating the internals, you can just skip straight to the Y per minute that you know it will produce. Ok what if they are interrupted? Well this is where you need to tweak the factory concept a bit, if they're interrupted you add a stall mechanic or some other punishment for missing the inputs. When you restart the factory the simulation is run again to tweak the new input values and output values as they might have changed.
So why is all this interesting (to people like me)? Because black boxing allows an almost ridiculous level of recursion, imagine a version of factorio where you zoom from the map to the factory level, zoom further into the design of an individual inserter which has it's own subgame for how fast it can grab etc. Zoom further into an individual subcomponent which also has its own subgame level. Each time you make a tweak or advancement the same rules apply, take the simulation, derive an output based on assumptions (e.g. X units of circuit board as long as inputs remain at Y per minute) and then zoom out. This would radically change the way the tech tree would be implemented, instead of research points to create the fast inserter you'd refine the existing one until it's subgame was giving you an improved X grabbed per Y figure.
Ok so what about these subgames? The best examples of what these could be already exist as games in their own right which is those produced by Zachtronics (forum rules prevent me from linking, just google "Zachtronics")
Hopefully that all made sense and even better sounds enjoyable to someone other than just me