I usually end up specializing a few troop production centers, and focus on economic upgrades everywhere else. A typical build sequence for a given city tends to look like this:
  1. Religious temples, to quell the unrest when initially conquered
  2. Income: port, market, academy (to reduce corruption), farm (even poor harvests produce revenue, and larger populations mean more tax revenue), then sewers/aqueducts/etc (as the population increases)
  3. Happiness/Order buildings, since this lets me set higher tax rates (a happy populace is a profitable one)
  4. Garrison: basic infantry training buildings, especially in the largest cities (recruiting can help hold down the population growth/unrest, and they often need a larger garrison anyway)