While I enjoy the idea of leveling up your cities, the buildings that you are provided with are far too random to put a particular plan in motion (and thus develop a strategy) and their bonuses in some cases are lackluster. I suggest a similar 'leveling' system to heroes. That is on the first level up you choose a 'path' and that path opens up new buildings and building choices on level up for you. Say for example the paths are:
Growth (Chance for prestige, food and growth buildings)
Military (Chance for military, unrest and production buildings)
Technology (Chance for buildings that increase tech and provide minor new unique techs)
Trade (Chance for city gildar, caravan trade, diplomatic capital and treaties bonus's buildings)
Magic (Chance for buildings that produce crystals, shards, mana/turn and free city spells)
Keep in mind that city levels need not be limited to a single building choice, but the very first thing that needs to be looked at is balancing the buildings with one another. I find that I =always= build gallows, as the benefit of +10% production or +10% research is easily trumped by providing both of those things through reduced unrest. The bakery is an example of a good building. It is not 'always' a good choice but is strong enough on it's own that I want to shoot for the next city level to get it.