I've given this some more thoughts, and I'm convinced that a good way forward would be to scale everything up, including time. It'd play out more like SimCity, with some basic actions taken and then a lot of fast-forwarding. With support for some sort of supply lines and seasons. With seasons things can get really interesting strategically, and it helps make the game not too boring at any time. A gameplay that's more automatic, like some sort of huge-scale Caesar game, but where you can give a lot of input on a lot of things if you want. Basically make it a game about supply lines with real season support and things will get interesting.
But really I'm also quite convinced that it's nowhere near being possible with the speed of current computers. It would require too much dialing down.