I think a better solution to Map Clutter would be to restrict the ability to exploit the map to more accurately portray Human Impact on the map.
Instead of arbitrarily spacing out cities, reduce the radius that the city can exploit tiles until later Technologies and Improvements extend transportation and reduce the number of early places you can place a viable city. No large city before railroads, for instance, was far from a river or a coast, preferably both or several rivers. Any other position required major infrastructure to provide water or the city stayed small and insignificant.
That would force the player (and, hopefully, the AI) to choose city sites carefully until the Industrial Era (over half-way through the game, effectively), so that while there might be 'clusters' of cities in really good areas (like the watersheds of the Tigris-Euphrates, the Chinese Yellow and Hwang-Ho river plains) large parts of the map would by necessity remain the province of smaller 'settlements', camps, Improvements, etc for much of the game.
IF in addition we require City Districts to be contiguous so that each city must be a compact single entity and relegate everything else to sub-city and partial tile settlements, camps or improvements, and I think the map will automatically be visually 'decluttered', at least until late game technologies make populations soar and the modern sprawling Megalopolis (Megalopolae?) possible.