I think that we cannot get 1000 city states, it would lag horribly and make the world diplomacy too complicated. so i prefer gameplay to historical accuracy srry, i just think that few powerful city states would be much more enjoyable than tones of little shits:
Asian cities:For china one or two at least(one tibet, one south china), more would make the game too complicated. One in south west asia (angkor). DOn't know for mongol capital because if you want to represent mongols by barbarians so they will destroy it! I think that very powerful barbarians would fit better in waiting of a mongolian civ. Maybe two cities states in central asia to represent samarkand ect...
One in south or west india. For middle east, i think that there must be jerusalem and maybe a phoenician city, another to represent iraq(babylon or bagdad in medieval area). And maybe one last in arabia with tons of petrols around to make some of these cities very interesting for colonials powers. After i just don't know for byzantines in medieval area, do you want to make them city states or as the roman civ? For russia, would be cool to see kiev.
South america: Just one or two cities to represents incans, the rest(bresil ect...) should only get barbarians.
North america: Do you want to make the iroquois? In all case there should only be barbarians encampment(except in mexico) to represent the nomad lifestyle of amerindians or maybe just a city states in classical area to represent the pueblo(you know, the big cities scuplted in mountains that look like helm's deep), or an other to represent hurons(iroquois worst ennemies) to challenge the iroquois if they are in it.
tlaxcala: I know this is the city that destroy aztec empire(spanish armies was 5% conquistadores, 95% tlaxcalans) but, she's just too close to mexico.a barbarian encampment would fit better, so at least one city to represent mayans.
africa: I just don't know if you want to make the songhai or the malinese. If this is the songhai then their capital is gao and not timbuctu, so timbuctu should be a powerful city state, and then there would not be civilizations in africa before 1450 at least!!!
To represent ethipian, there must be at least one city state. The rest of africa should stay barbarians(except one city states for the great zimbabwe in classical area maybe...). ah and for north africa we need at least in classical area carthage!
Europe: We must create a civ to represent spain(like the guy who already created a celtic civ), city states cannot replace this world power(especially for the colonization). Also, two city states in east europa(warsow and budapest) that would make the german-russian relation intersting, two in italia(for medieval area), Rome and Venice maybe??? One in south italia(siracusa for classical, napoli for medieval?). One in greece for medieval area(athens) and Edimburgh, lisbonn and amsterdam of course. Like the mongolians, barbarians encampment would perfectly fit for scandinavia because if you put city states then they will not be agressive at all. Or maybe just one in denmark.
But there still tons of unanswered questions: What will become a civ when she exploses? tons of city states? Will you recreate an independant civ just to represent civ that explosed? How the world will be? With the exagon it should be at least two time more large than the civ 4 one! It will results lag? certainly, i just still don't know what about the fact that civ 5 can fit will multicore. It will certainly reduce lag for me with my quad core 3 ghz but for the others???? Maybe you will be obliged to accelerate the construction times to permit player to build big armies(with the exagon it's just necessary now, you can't invade the half of europe independant city with 3 units and a catapult empiled

).