Interesting. A while ago, I was also thinking about making a 'physical' World Diplomacy map, and I now plan to try to rebalance the current World Diplomacy map in the summer, but just for purposes of online play.
I agree that the world map has problems, but to be fair, I don't think there are any easy fixes. Your example in which you would remove South-Africa from Antarctica but won't change anything else on the map wouldn't make sense; not only Frozen, but also Argentina would be too strong if you did that. If you want to make changes, many different changes at once need to be made, and not just changes regarding supply centers. Most of what's wrong with the world map is due to powers having too few attackable neighbours, and to fix that, huge changes to neutral areas need to be made.
Let me give you one specific example. Pacific-Russia borders Russia, but doesn't have a large front with him, which makes war between these two unlikely in the early game. Pacific-Russia and India should border, but there is a ridiculous amount of neutral supply centers between them, so war between them is unlikely in the early game, too. Pacific-Russia should also border Western-Canada, but doesn't, which makes war between these too also unlikely in the early game. This leaves China as the only real viable option for Pacific-Russia to attack. Guaranteed enemies are bad for the balance of the game and this is why China is the worst country on the board. You could fix the situation by significantly reducing the number of areas in central Asia, or just create an entirely new central Asian power, and by making a water territory that borders both Pacific-Russia and Western-Canada.
But these kind of changes require a lot of time and skill to do properly, and they need to be done all over the map. It is for this reason that I delay this project for myself until the summer. It's also why I would suggest that if you are not willing to spend a lot of time on the map, I suggest changing nothing at all - for there are no easy changes. Or, if this project of yours is in no rush,you could wait and we could look to it together. :p
For your interest, here are some statistics about the world map: http://webdiplomacy.net/forum.php?viewthread=1460060#1460060