I guess I'll kick things of with a few half-baked ideas; I really haven't decided on any percentages though.
Because city-states are going to be the main drivers of diplomacy, this is what I think:
I'm going to move from east to west:
Nearly all of China's diplomacy will probably be with city-states:
Seol, Korea
Lhasa, Tibet
City-States along the Silk Road in Central Asia (Merv?, Smarqland?, Turfan?
If the map is large enough:
City-State in Manchuria
City-State in Vietnam or Khmer/Cambodia
I'm not sure what to do with the Indian subcontinent. Perhaps Pataliputra could be a city-state?
Moving on to Mesopotamia:
If Babylon is not in the mod then it must be a City-State;
If the map is large enough, then Ur/Sumer and Nineveh/Assur could be included as well.
Later when Arabia spawns, Sana'a or Masqat could be city-states
Nubia/Ethiopia/Kush must be represented as a city-state as they interacted heavily with ancient Egypt (Kerma/Napata/Meroe)
The Middle East also needs Jerusalem, a Phoenician city (Sur, I guess), If the map is big enough we can have Anatolian cities (Troy, Hattusa, Gordium, Sardis) and Knossos.
No Carthage Civ means City-States will have to suffice for North Africa & Iberia (Tripoli, Carthage, Rusadir, Gadir etc)
I don't know if a city-state in the Balkans/Illyria/Dalmatia makes sense; same goes for Gaul.
(I don't know if it will be better to model Greco-Roman influence through military conquest or through settling)
For Medieval Europe:
Edinburgh or some other Scottish city to spice up England's Medieval game. Same goes for Dublin or some other Irish city.
If the map is big enouch Antwerp might be good. It'd make the Low Countries interesting.
Probably a Polish city-state is needed in order to let Germany and Russia compete for influence.
I don't know if Germany will model the HRE or Austria, but Vienna or Budapest might be additional city-states; same goes for Kiev.
After the Vikings (Barbarians) stop raping and pillaging, they probably should "settle down" in City-States such as Copenhagen, Trondheim, Oslo, Stockholm etc.
It's too bad that there are no Iberian Civs so City-States will have to fill the space; maybe have city-states in Seville, Lisbon, Barcelona, Toledo (not Barcelona).
The game will have to model "what if the Spanish Kingdoms never united during the Reconquista?"
For Mesoamerica:
Montezuma might need to interact with Chichen Itza, Tikal, Copan or some other Mayan City-State. If the map's large enough maybe Tlaxcala and other altepetl can be included.
Andean city-states are a must including Tiwanaku, Chan-Chan, Cuzco
In sub-sahran Africa, there should be Mapungubwe or Great Zimbabwe.
In Oceania, I'd like to see something on Easter Island as well as maybe Jakarta on Java.