Citizen micromanagement is key, the governor is ********, and will not have the same goals as you, micromanage every citizen to maximize growth up to happy cap, then emphasize the cities goal. Personally I control the work of Every citizen, in my empire. My current game is empororer/large/marathon, having over 60 cities.
Worker automation is also a very poor choice, except late game, where you have nothing to do until railroad/repairing random pillaging. At that point worker automation is helpful, assuming you have leave forests/old improvements.
A good way to do things, is looking at a city every time it finishes building, or if the time till growth of a small city is delayed, it may be a good idea to find out why, and afterwards if you notice a tile that is out of place, send a worker to come fix it. Sure its tedious, and some may find this boring, but trust me the results will pay off well.