While I enjoy the great diversity and specialization for towns to build and construct whatever building in whatever location, sometimes I feel that some of the buildings are out of place. If someone has already suggested something like I apologize and also I haven't fully worked out how this would work as it's just an idea. Sizes referenced are the sizes used when constructing improvements to a city (1 normal square is 4 smaller squares or 2x2 plots).
Districts. When constructing buildings you must first build a respective district by building a sort of 'base building', which would still take up only one small square, but otherwise prevent other non related buildings from being built in the 2x2 plot set aside. In other words you cannot build a merchant stand and a barracks in the same district as they are two different types of buildings. Therefore whenever improving a city, you would first select a district, select the appropriate improvement, and then construct it.
Cities will at first be restricted to a certain number of districts and a limitation on types of improvements, but researching related techs, such as Economics would increase the number of 'Merchant Districts' that can be built for a given city. Additional increases can be achieved for individual cities by building certain World Wonders, such as the Great Mill, which already take up a 2x2 area.
Lastly some improvements can be applied to different types of districts, but take on different specialties. For example, building a weaponsmith or an armorer in a military district would not only reduce production value and increase upkeep, but also provide a small bonus to unit strength and defense in the associated equipment. However building these improvements in a merchant district will still provide the reduced production values, but may no longer require upkeep and instead reduce hurrying costs of training units and reduce the wages of stationed units.
Off the top of my head some of the district types that could exist are, Merchant, Military, Civilian, Production, Agriculture, and Magic.I'm not quite sure what do about diplomatic and some miscellaneous 1x1 improvements, but most improvements that already take up 2x2 area require higher techs and could be considered a district to take up a spot.
Again this is a loose idea so any other suggestions are welcome. A friend of mine just suggested that by having multiple military and production districts there could be different 'production lines'. There would be the main city production line, which works the fastest and can build improvements and units, including pioneers which are restricted to the main city production line. But there would also be a slower district production lines which are based off of an individual districts improvements. So a production district with a workshop could slowly improve itself while the main line and the military district are producing warriors for a battle. Either way, this would be a massive revamp.