I think this is a great idea Linkman, I've always had trouble tossing up between different mods each time I start a game.
There are a few small things that have always bothered me about the base game, and while I could always change them myself, I figure I may as well make them public in case you are still taking suggestions.
1. If you are including older religions (i.e. Hellenism), then you really should give Shinto to the Japanese. Not only was it their indigenous spirituality, but is still practiced alongside Buddhism in the country by over 100 million people. Indeed, much of their history and actions as a nation have been directly influenced by Shinto
http://en.wikipedia.org/wiki/Shinto
On a similar note, maybe a religion to represent that followed by the Aztecs and Mayan before the Spanish conquest. Again it was largely the aspect that dictated their entire lives. It would give them something in common, a connection between the different Native American civs. It would also add an extra reason for them to argue with the Europeans once meeting them, which is pretty much the way it happened in history.
2. There is currently no fresh water in the Yucatan Peninsula. While it is true that there are no large rivers or lakes in that area, it is over the worlds largest underground fresh water river system. The entire area is completely covered in fresh water cenotes that were the source of fresh water for the Maya. Every single notable Maya city was built next to one of these cenotes. Thus I find it annoying that when playing as the Maya I have no source of fresh water in my cities, when they should. Is there a way to add fresh water to the tiles in the peninsula to represent this?
http://en.wikipedia.org/wiki/Cenote#Cenotes_and_the_Maya
3. Lastly, and again on a similar note, I find it strange that the Maya can't settle in Jungle, or chop it down. It prevents the founding of cities in many areas that they historically inhabited, and I'd say that most of their cities were built within the limits of the jungle.
I'm not sure if this link is very useful:
http://en.wikipedia.org/wiki/Classic_Maya_collapse#Drought_theory
but the Mayans were known to have chopped down or burnt away much of the forest and jungle surrounding their cities. Some even believe that this is what lead to their downfall, because their removal of all surrounding jungle led to a loss of soil fertility that turned it unworkable.
As you can see, I'm a bit of a Japan and Central America history buff, so I admit that I'm probably the only one who cares about these things, but I just though I'd see if anyone else was interested
Thanks again for the work you're putting into all this!