I have been playing a lot of Beta 2B, and the city management seems to be playing near the "spam identical cities" chasm. I think this is due to really NEEDING a food resource to make a city work and because its Beta and their are not enough options for buildings to make you really have to choose. I think this could be improved by the following:
Gardens: limiting the number of gardens per city was a really good idea, it makes food resources more valuable. However I think the current limit of 1 is TOO limiting as until you get Civ food techs going on a resource tile or two, your cities are not very useful. I think the limit should be 2 gardens per city; enough to allow a city to become interesting, while still requiring food resources in your empire to support large populations and high level cities.
I think having more buildings that force you to make a real choice about resources would add a ton of flavor and strategy to city building. Most of these could require being adjacent to another improvement or at least having that improvement in the city. This will allow for city specialization and force strategic thinking as you could NEVER build all the building available in any one city. Some potential ideas (numbers are suggestions but give the idea for the purpose of the building):
Farmers Market: one tile, requires Market in city, available with Economics, one per city (uses 4 food, give 3 gold and 1 pop growth)
Mead Hall: one tile, requires Bee hives, (uses 4 food, gives 3 gold, 1 prestige)
Brewer: one tile, requires Wheat (uses 2 food, gives 1 gold, 1 prestige)
Tanner: One tile, requires Workshop, requires Equipment from Warfare tech tree (gives 2 material, reduces city growth by 1 person per turn [bad smell])
Potion Makers Workshop: One Tile, requires School, (uses 1 material, 1 metal, 1 crystal give 3 research)
Bog Iron Smelter: one tile, requires swamp tile, requires Forging (Uses 3 material a turn, gives 1 metal)
Clothier: one tile, requires Market, (uses 3 material, give 1 prestige, +1 population growth
Painter: one tile, requires School, (uses 2 gold, 1 material, gives 4 prestige)
The idea is to have enough options that every city building decision matters because of what it will do, AND also because of what other options it will prevent me from being able to develop.