This may be some what repeating what others are saying but the premise is correct; the order your cities are in, is the same order they were created on the server with oldest being at the bottom (if u take/lose cites this gets reset after maintainence)

For example I start on the first day of the server and i am right next to a level 10 npc that was there when i got there. Now as i build more cities my main will stay at the bottom. But when i eventually cap the lvl 10 next to me that city will now be at the bottom because it was created first. Same thing for players cities.