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The documentation below has been compiled by Markos, to help you get "the most" out of your CTP-based creations.
Up to 32 civilizations in a game
It turned out to be a piece of cake. Userprofile.txt stores various game settings, like the resolution or the gameplay and sound options. And, of course, the number of civilizations that can be in one game! The very first line is "NumPlayers=8"! There are also two more settings, "DefaultCivIndex=16" and "CivIndex=16", which obviously have something to do with it...
If you change it to 16 for example, when you start a new game you will see the civ settings saying "16". Dont try to change from within the game, because it will just crash (in my build anyway). Once you start a game everything works as usual, just slower. Depending on your machine, it will be a little slower to a lot slower. With 32 civs, you'll need a REALLY good machine if you don't want to wait.
Colors.txt
Colors.txt defines the colors of the civs. The first player (human) always takes the blue and the rest are set randomly. From colors.txt you can change the default blue (and all other colors) to whatever you want.
Civilization choices
Two text files define the choices you have for civilizations. The game has 42 civs, with the barbarians included which means that on the screen where you choose you civilization you will see 41 choices. A comment in the text file says that you can have up to 64 (63 to choose from). Unfortunately, if you have more than 45 you will see only the alphabetically 44 first. I suppose that computer will still be able to choose for the AI one of the civs that are not shown though. Still, you can always replace a civ...
Graphics
Bad news, good news. The bad news are that terrain graphics are in some .til format, and units and city ones are in .spr format. The good news is that Activision is working on some way around this, probably with some sort of converting utility. However, pretty much everything else, including monument screen, alien project and credits graphics, are in .tga format, which is a very common format.
Adding units
Guess what, units.txt allows you to change unit info.
I'm not someone with big experience in game file editing, but I was able to have more than 128 units! The best was that they showed up in the Great Library! There's a lot to discover by people more experienced than me but I think that you can do similar things with advances, city improvements, whatever... AI files
There lots of editable with Notepad .fli files, which contain information on the behaviour of the various AI personalities. There is a LOT of stuff to look into and experiment, the good thing is that there is a readme file(!) that explains a couple of things.
In general, Activision will soon have a section on the official site about map and scenario editing. Hopefully, we will see some modifying guides, either from Activision, or eventually from the fans...