Personally, I think a few "great" cities should be able to make it to the hundreds of thousands.
I think we should keep in mind that the game is about an almost destroyed world getting back on it's feet. A city with more than a hundred thousand people in it should be very rare I think. I've been trying to find some exact numbers about city population in our medieval times, but can't seem to find many conclusive numbers but...
By the early 12th century the population of London was about 18,000 (compare this to the 45,000 estimated at the height of Roman Britain).
It is difficult to evaluate the population in Paris, in the Middle-ages. Around 80.000 inhabitants in the XIVth century the number increased to 300.000 in 1475
I did find an interesting website from someone who seems to have done some research for this, and made a site about population density, city density and so on for Medieval Fantasy Worlds. For those interested, you can find it here. Some numbers from that site:
Big Cities range from 12,000-100,000 people, with some exceptional cities exceeding this scale. Some historical examples include London (25,000-40,000), Paris (50,000-80,000), Genoa (75,000-100,000), and Venice (100,000+). Moscow in the 15th century had a population in excess of 200,000!
So, as I said at the start of this post, really big cities should be very rare and should require a big investment to get / keep them happy.