Yes swap factions are still planned for later.
As for the Greek states and cities, I think this would be the best distribution:
Greek cities faction: Sparta, Athens, Syracuse, Massalia, Boiotian League, Byzantion
Greek states faction: Achaian League, Aitolian League, Bosporan Empire, Cretan League, (Thessalian League)
This has the advantage of most ''cities'' actually being cities and ''states'' being the Leagues. Furthermore, it's based on political alliances and oppositions:
Athens was allied with Sparta during the Cleomenean War, the Achaian League fought against Sparta, the Aitolian League fought against the Boiotian League, Syracuse was always quite close to Sparta, Sparta had a campaign on Crete, the Aitolian League made war on Sparta once etc.
Later with our new map we'll have to see if and where other Greek towns that are still rebel territory right now (Apollonia, Sinope etc.) fit in.