It would be nice if some use could be made of the automate city feature without immediately setting fire to your civilization; maybe a inbuilt queue of good things for general cities is a technical solution. Some buildings get better or worst in some times, but the choice between toolmaker vs mining camp isn't as controversial as the governor immediately going for that Sweet Magic Evil Gold that is the Assassin's Den.
I think with those sort of cities(cities for the sake of having cities) you go into the big build menu(and decreased icon size in later ages) and manually spam click all of the good icons and then research for a while. It's a bit repetitive, and some icons are a bit hard to decipher even after playing a long time.