(FIRST POST EVAR!)
Just thinking about some indigenous civs that have shrunk or superceded. Justification in brackets.
Fez - Cultural (Historically dominant city of the area)
Lagos - Maritime (Centre of Yoruba people)
Mycenae - Cultural (Massive civ centre in Bronze Age)
Hattusa - Militaristic (")
Balí - Cultural / Maritime (Not needed if you're adding Jakarta or Manilla as well, but may work otherwise)
Hokkaido - Militaristic (Very different and separate from Japan itself and has co-existed rather than been a menber of it; as pretty much the only new option in the area I could think of,may work if running this on a true position.)
Colchis / Tbilisi - Cultural (Again more a client to successive powers than a smaller province, and has been culturally important for 4000+ years.)
Babylon - Similar to Hatussa / Mycenae.
You may've noticed most are concentrated around the Near East and the 'Fertile Crescent'. I'm trying to make a scenario and map of Civilization's Cradle from North Africa to Iran of thereabouts, and these are the citystates I was gonna litter all over the place. Big shout to Opera for great work.