Do we really need cities in every language? I can't think of a game where I don't run into problems where my cities are outside their 'proper' tiles and thus can't be named properly. Just get rid of it all and name cities in English (this is already done in the far east).
An exception to this is if the names change in an English context; New Amsterdam to New York, for example. Certain ancient cities could also be renamed as more era-appropriate ones after conquest, which doesn't always happen in the current game. Hillah for Babylon, Tripoli or Beirut for Tyre, Tebriz for Hasanlu, Cairo for Fustat. Think about it.