Wow great stuff, we're really happy to have you doing this. Thanks for posting that info. As I mentioned via PM, your 1940 map is the best oversized/civ heavy map I have ever played for a number of reasons, so I for one am glad to see you using it as a base.
I think the cities you have on it are near perfect as is. The areas I would suggest you consider altering, would be as mentioned Israel/Palestine and to a lesser extent, the Koreas.
Personally I think it would be best to try to get in 5 or 6 cities in Israel/Palestine to best represent that important conflict, which is why I suggested increasing the land area if possible. The two have populations of about 7 and 4 million respectively.
Gaza Strip as the capital for the Palestinians, and East Jerusalem. (East Jerusalem is the proposed capital for the Palestinian state, but that does not exist yet, was the idea here).
Jerusalem as the capital for Israel, along with Tel Aviv, and whatever other 1 or 2 cities work best for placement.
I'd be very interested to hear what you think about this, and any other areas.
edit: Sorry, somehow I missed your posts right above on this topic, I am an idiot. Ok, so we can only have one for each? Can we make it into two each by having them extend into the regions that are in reality Lebanon and Jordan?
Anyway, just a thought. I'm sure whatever you decide on will work best.