By recheacking my thread title, it might better be called, "centralised production".
The first time I played civilisation, I found it very weird that everything was organised by cities. At that time, I remember saying that in an area, there could be way more cities available. It became even more illogical when playing on a real world map which for example, allowed you to place at most 2 cities in england.
So my suggestion is another way of doing things that could bring other problems of their own but it might interest some people. To visualise it better take civilization IV, remove the cities and only keep the tile development. Which mean that all development and production is done by devloping a tile (placing a mine, placing a farm, etc) some tiles would have houses with population but they are not a central city, there are spread as you like on the map. Tile with population might also have different levels of density.
So it creates the idea of developping and changing the land. Since there is no centralised production it would mean that everythings that control your production will always affect your whole empire since it cannot be divided by cities.
How would you produce? You empire would give you a production income and you pay for what you want to build by spliting that income in various tasks. You could be allowed to place development tile from X squares from your current population tiles and you could place new military units in population tiles.
For combat, it can become complicated if there is a tactical map. Because there is nothing that clearly define what is a city, so the whole map can be a battlefield. Cities could also eventually fusion together and become 1 city.