First, I'd like to mention this is my first time visiting here with an account and therefore my first post. (I know it says I registered November '08, It's a long story, better to leave out)
Anyways, I'd like to congratulate on finally splitting up the EU somewhat, Now I'll be able to play... as POLAND (Along with Canada)! Awesomesauce.
However, I do think having Switzerland as it's own civ is rather pointless in my opinion (Apologies to all Swiss out there). It's so small, it's going to be one city civ (If that's wrong, then, please, do show a map). Also, as not a member of EU (and the diplomatics of IV), Germany, Italy, and France could look forward to and conquer it 5 turns Max with some nice tanks.
I believe Switzerland should become a minor state, and I have some new countries (Also, since their is only 48 out of 50, you could do one or two of these and leave Switzerland alone).
My first is to separate Vietnam from ASEAN. My reasoning's for this include that it has, for relative for it's size, an extremely organized military that closely resembles the Pepole's Republic (Even being called Vietnam Pepole's Army). Due to this, it has a more efficient military compared to it's neighbors, and due to the unstably of the area, could lead to back stabbing between the nations. and Vietnam could be a serious contender to rule a good chunk of Southeast Asia (Until China invades the area, that is.) Now, your probably asking yourself "Well, It's also a small country, probably 3 starting cities at the most", but think to yourself, "Can Switzerland /really/ hold off Germany, Italy, or France If a wars does happen?"
Leaderhead:
http://en.wikipedia.org/wiki/Nguyen_Tan_Dung (I think he should be easy to make. Just take the body of Teddy, turn his tie blue and his suit jacket navy blue, make a good head and some custom animations and your done)!
UU and UB: I'll only look into these if you are st least looking to go use Vietnam (Same goes to all civs mentioned here)
Before I tell my next idea, can I ask Mongolia's fate? I thought it was going to be playable, but now I can't find it anywhere in your list, not even minor or failed). Anyways, I bet you can tell that the Khan's homeland is my next idea, for that reason. This is almost purely for Genghis Kai, as a "We're sorry we're not using your map which you worked hard on anymore. Here's a small token of our appreciation for giving up your time", but I can think of some good reasons to make it playable (If already not). If it's a minor, it's going to get killed by China or Russia, and that could potentially cause a WW3 very early between the two Red-colored superpowers. If it is it's own country, this could forestall a war (As AI isn't as likely to attack a civ then a minor state), possibly changing what countries start it. It does have a good army, but it's not as strong as Genghis Khan's armies. Finally, I'd love to hear Mongol Internationale in the game, It's such a beautiful song

. (Note: Both Khan's themes IS Mongol Internationale in the actual Civ 4, so if your cheap, you could just use the late version of it).
Leaderhead:
http://en.wikipedia.org/wiki/Sanjaagiin_Bayar (Your going to have to google his image, it's not there).
Finally, I also think Ghana should be a civ. I think the reasons why are already stated. Plus, Africa should have more than 5 civs that are actual countries and not allainces.
Leaderhead:
http://en.wikipedia.org/wiki/John_Atta_Mills
That's all I got for now, and I understand if your too far to edit Swissie and that if you keep on using every one's ideas, nothing will get done.
I'd also like to help mod, but my skill is literarly none, so I won't.