Well summarized Hellgrim!

There is one point though that haven't been touched upon yet. When under attack from stronger players, they like to take out your MAIN city first!

So if you avoid building certain buildings in your secondary towns, you could stand without those alltogether if you lose that city.

This could seriously harm your research progress if you are still researching, and you could move backwards many levels of technology because you don't have the required buildings anymore, leaving you even weaker in battle.