There is a lot of overlap between the 600 AD and 1700 AD scenarios; for the most part, the way that 600 AD plays out tends to replicate 1700 AD's city placement rather well. The same isn't the case for 3000 BC to 600 AD. Most of it surrounds the Alexandrian conquests wiping out much of the old cities, which for a historical simulation I imagine should happen in a majority of cases.
First, I suggest moving Egypt's settler 1S from its current starting position in v1.12. It will still settle modern Luxor, but in a more historical position. Then, they should most often next settle Memphis (otherwise no Cairo later).
If such scripting is possible, I think AI Greek conquest in the window of the Alexandrian conquests (i.e. when they get armies spawned in Egypt and Mesopotamia) should also script some changes to the cities in those areas. If Memphis is conquered by the Greeks in the turns after their armies spawn, Alexandria should be auto-settled. An ancient world game with Alexander conquest but without Alexandria just looks wrong. If Babylon is conquered, it should be auto-destroyed and auto-replaced with Seleucia 1E. When (or if) the Persians, Romans or Byzantines reconquer it, it would rename to Ctesiphon, and rename to Baghdad on Arabian flip. If Tyre is conquered, it should be auto-destroyed and auto-replaced with Antiochea ad Orontes 1N. Beyond the Phoenicians, Antioch played far more historical significance than Tyre, and it's better for gameplay as it doesn't crowd as much with Jerusalem.
Everywhere else should be good, I think, except maybe also spawning indy Merv and Herat later on, and they tend to not be settled by the Persians, since right now only indy Samarkand is spawned on 3000 BC.
Thoughts?