Some of the missing countries have data on citypopulation:
Paraguay: Asunción, Ciudad del Este, San Lorenzo, Luque, Capiatá
Peru: Lima, Arequipa, Trujillo, Chiclayo, Piura
Syria: Aleppo, Damascus, Homs, Latakia, Hama
Maybe you don't want to mix sources but worldpopulationreview.com has the other countries:
Burundi: Bujumbura, Muyinga, Ruyigi, Gitega, Ngozi
Panama: Panama City, San Miguelito, Tocumen, David, Las Cumbres
Qatar: Doha, Ar Rayyan, Umm Salal Muhammad, Al Wakrah, Al Khawr
I might be wrong but for China I think you've listed provinces. I believe the cities should be Shanghai, Beijing, Guangzhou, Shenzen, Tianjin, according to citypopulation
Perhaps use Seville for Sevilla (as with Naples not Napoli) and allow Belize as a type-in for Belize City (as with Mexico, Kuwait). Also, maybe use the modern name Nur-Sultan for Astana.
Anyway, just suggestions! Again, great quiz!
Secondly: Burundi, Panama, Paraguay, Peru, Qatar and Syria has been added
Thirdly: China, Seville and Belize City has been fixed
Fourthly: I am aware of Nur-Sultan, but as Quizmaster said "we're not in a rush to bend over backwards because of some third world despot."
Ones I thought might be relaxed a bit: Argentina: Tucuman, Azerbaijan: Sumgait; Bulgaria: Ruse; Cambodia: Siem Reap; Iran: Mashhad; Iraq: Erbil (I know Kurdistan a bit so knew its alternative names like Arbil and Hawler). I used all these fairly standard transliterations/ versions and got knocked back.
There's another issue with large metro areas, to which there's no ideal solution. For Oman you've used the constituent bits of Muscat metro area, while for other countries (Taiwan, Philippines) it's the whole city rather than the very large component parts, some of which are larger than the 'core' city (New Taipei, Quezon City).
There's also one area not covered - Palestinian Territories. It's probably doable without starting arguments about the status of Jerusalem!
Here's one definition for Palestine http://worldpopulationreview.com/countries/palestine-population/cities/ but I've seen much higher figures for Gaza city and Israel also claims East Jerusalem.
You've done an amazing job on this quiz! You've put a lot of effort in and it's interesting and challenging. It's told me some stuff I didn't know (for instance, I'm sure most non-Sri Lankans like me would be surprised that Kandy, the non-Colombo city most of us have heard of, is smaller than several others!).
Thanks and appreciation to you.