Areas:
Abyssinia and Mali:
Abyssinia really depends, Aksum for very early period, but then again ethiopia was always rather tribal during ck2 phase and also past it, the important cities were the cities of muslim sultanates as well they were coastal except for harer, which was actually the biggest medieval city of that region. The Nubian cities of that time are not rly significant.
Mali on the other hand it is mostly timbuktu, koumbi saleh was also big at some points and well the gold cities were the cities of control and they lead to power, but to my understanding they were not as big as the other 2.
North Africa:Tunis and Fes were the 2 biggest cities during the time of ck2, they were rather big cities for that time with 100000 citizens, Tlemcen was also rather big, besides those there was marrakech, meknes and sijilmassa, but not on the level of the previous said. Cities like algiers or oran were not that big and libya was kinda in decline already before maghreb got into it, but then again libyan cities might still been of some size at that point, but i doubt it.
Arabia, Syria and Anatolia:
In case of arabia yemen was the most densely population and so cities like aden, sana, ibb were in comparison to other arabian cities bigger, mekka was big as religious center, while suhar and muscat were big as centers of trade. The capitals of dynasties in yemen were probably the biggest at most times as the region was by far the most fertile.
Syria had Damascus, Aleppo, Homs and Hama, Damascus was probably the biggest at that time, jerusalem was also there, but i doubt that big.
Anatolia had Nicaea, Sivas, Kayseri, Konya and Trebizond, Trebizond was probably big for the longest time, while konya was probably the biggest at most times in challenge with coastal byzantine cities, but here my knowledge leaves me.
Balkans:
I guess this includes thrace, so well constantinople was the biggest, then we got sofia and thessaloniki(not sure on this), ohrid was big in late middle ages, same for prizren, nis was fought over a lot and belgrade seemed important as control point.
Italy:
There is rome, venice, naples, palermo, messina, syracuse, genoa, florence, pisa, verona, milano and bologna which probably were all rather big, rome was never the biggest, but always big, venice was also never biggest not during ck2 time or after, naples was biggest past ck2 time and maybe even during end of it, palermo might been biggest for a short time during unified kingdom of sicily, but was then overshadowed by messina in sicily, syracuse was rather big at start of ck2 time and might even been biggest there as others had yet to grow, genoa was never rly biggest, same for florence or pisa, verona, milano was not big enough during ck2 time as it was in contension with other lombardians, bologna i named here because not many know it was one of the bigger cities during ck2 time in italy.
Iberia:
Cordoba was probably the biggest city Iberia ever had during medieval times and according to some biggest in world for some time, but i doubt it, it was biggest in europe though. Granada was biggest past fall of cordoba for whole ck2 time, other big cities were lisboa, sevilla, toledo (more a symbolic city), valencia, barcelona, alicante and roussilon, but granada was rly bigger than rest of them past cordoba during ck2 and even cordoba was still bigger than them.
France (de jure area):
Paris was the biggest for whole ck2 phase, past that comes rouen, toulouse and montpellier, south france was more urbanized and so also had bigger cities, bordeaux, lyon and the cities in provence were the next level to that.
Holy Roman Empire (de jure area):
The biggest city was cologne followed by cities like gent, brugge, mechelen and then regensburg for a big part of ck2 phase. Prague was biggest at end of ck2 phase, lübeck, hamburg and bremen at one point were racing behind that, worms, speyer, trier were big during that time aswell as mainz, the center of power of hre was in that region for all of ck2, brunswick was the biggest city in north germany, while south had augsburg, ulm, nürnberg (the biggest in south at end of ck2) and munich, but i think i am talking too much now and yes wien also existed.
"Carpathia":
Esztergom was biggest pre mongols, kosice and budapest past them, ragusa was also big, maybe bigger than those 2.
British Isles:
I honestly dont know, london was there, york also, but cities in east england on coast might been the biggest.
Scandinavia:
Lund and bergenhus directly in scandinavia, but the biggest were probably in schleswig like ribe and one i dont get in my mind right now.
Poland, Baltic area:
Krakow, breslau, danzig existed at time already, but the center of poland was in greater poland, so the biggest city was probably there, breslau was biggest city when mongols came and past it till krakow and danzig passed it past ck2, baltic was well tribal.
Russia (including Belarus and Ukranie, but not the steppes):
Kiev was biggest, novgorod was big, same for smolensk, suzdal and chernigov, moskov was insignificant at that time and even past mongols overshadowed by tver till russia foundation.
U said no steppes but at begin of ck2 that region probably contained biggest city (khazaria) and later sarai was biggest under mongols for sure, but probably not so big as wikipedia says, astrakhan was also not to shabby.
Persia:
Baghdad was the biggest city and the biggest city in the world for most of ck2, samarra was big at short times, kirkuk and mosul were big.
Persia itself had Isfahan, shiraz and the biggest at start of ck2 was probably a city in khuzestan like ahvaz, tabriz was biggest in north persia past mongols.
The east contained merv, herat, urgench, samarkand, bukhara and kabul, all rather big cities at that time and center of science of world pre mongols.
The Rajastan:U will need someone else for this region.
