Similar to Sub
When I still played un-modded I would rename everything including civ name. The city names were then related to my chosen theme.
eg
Civ = Mystics
Ruler = H.P.Lovecraft
Title = MagePope
City names were then picked from locations or entities of Cthulhu Mythos
eg. Arkham, Hastur, Glaaki, Leng, Necronomicon, Nyarlathotep, Yog-Sothoth, etc
First City would usually be Haven, Eden, Spore, Genesis, Seed, Virus depending on theme.
I do have a nomenclature for cities from other civs, which is basically keep original name and add to it.
Name >Civ captured
Name >Civ* captured capital
Name =Civ flipped city
Name +Civ through peace negotiation
Name >Civ*RIP last city and therefore destroyed civilisation.