It seems indeed necessary to amend Firaxis proposed list of cities - I will certainly make my own changes in my game. Since you propose to do this as a mod, I suggest you consider some technical questions which are - as far as I am aware - not yet answered:
- At what time are city states spawned in the game? At the very start? Slowly over time? Do different city states spawn in different eras? (I hope it's the latter)
- Will the game somehow check the list of either civilizations in the game or city names already used in the game to avoid double occurrences? (again preferrably the latter)
Whatever the case, it makes sense to restrict your list to cities which have historically been sort of sovereign or independent for a significant amount of time, earning the title of city-state. Not sure how this'd apply to colonial cities, for example.
For the above reasons, I would include cities that apply no matter whether they are part of any confirmed civ city list, as usually not all civs are in a game at the same time.
Some I personally feel are still missing from your list (my interests mainly lying in medieval HRE):
- Berne, Basel (both certainly more influential than Geneva)
- Worms, Speyer, Ulm, Lübeck, Konstanz, Regensburg, Rostock, Braunschweig (some of them may be on the German list)
- Besancon, Strasbourg, Metz (some may be on French list)
- Pskow
- Pistoia, Lucca, Pisa, Parma, Bologna, Siena, Amalfi, Verona, Padua, Modena, Vicenza (not sure which of them may be in the Roman list)