Really? In Your opinion code for city look algorithm is the most important thing to fix?
Then You will be really disappointed by the fact, that after reloading saved game it could move from one place to another. I think this might be Your biggest issue with realism problems in game. All these citizens will be really surprised, when they go to take photo of Statue of Liberty and it's not where it has been all these years...
To add some more serious info:
You have no idea, how many variables need to be considered, when creating such algorithm. City size, many unique buildings (wonders), how they interact with each other (many times walls go in the middle of building), how much land as available around city (ocean, mountains can interfere with that). It's not like building location have any meaning like in simcity.
In my opinion they did pretty good job with that algorithm, but it's just my own opinion as a programmer.