Great City Lists! Thank You! I, too, hate seeing Zimbabwe 2, New London 3, etc.
I came across one problem, though. I'm using the list of default civs to expand the list of cities for the normal civs and 2 other civs that I added (Inca and Australia). I'm playing America, and when I settled my second city, they wanted me to name that one as Washington (which I already had, obviously), so I get the 'You must use a unique name' message. I found out what was causing the problem. I had just copied the whole list and pasted it in the mod file and there is a space after some city names, before it drops down to the next line and next city name. When I deleted all the extra spaces, everything worked fine.
For example:
Washington_ <--- The _ is representing a space
New York_
Boston_
Should just be:
Washington
New York
Boston
The AI cities seem to handle it Ok, I think (haven't fully checked, though), it's just screwed up for the human player.