These have probably been posted before (and most are cosmetic changes) but here goes nothing:
1) Replace the 'West Balkans' Civilization with Yugoslavia (which I believe was existent during WWII), and the 'East Balkans' Civilization with Greece. It'll make a tad more sense (IMO). I've already done this in Notepad, so really small change, I guess.
2) Replace the Commonwealth in all the names with British or Great Britain/British Empire. A tad nicer to read, and though it was truly the Commonwealth during this time...whatever.
3) Give Reykjavik to Norway or Sweden. I don't see why the United States got it, unless it was to give it a Base of Operations in Europe.
4) This one is a major change. Taking the United States off the map and shifting focus to an enlarged Europe would do wonders for gameplay. Give the United States of America the city of Gibraltar or no cities at all initially, just soldiers. Or, make the USA a non-playable Civilization. While this sucks for people who want to play America, adding in America through python (if possible) at the time it joined the war would be (IMO) pretty cool. It would allow for more action in Poland, Greece, Italy, Sicily, etc.
5) The Civics should probably be changed to Ideology, Propaganda, Corporate, Labor, War, and Economy.
Ideology:
Propaganda:
Corporate:
That's all I can think of right now.
This is an awesome scenario/mod, and I can't wait to see the next installment!