I'm pretty new to this myself, but this is what I've gathered so far:
You can change the names of the governments in rules.txt. Before you get to the list of different tribes, and their rulers and attributes, there is a list of the governments and the default titles for these. In this list you can change the names and titles. As a simple change I changed:
Fundamentalism, High Priest, High Priestess
to:
Theocracy, High Priest, High Priestess
I'm also trying to make further changes, and implementing a government called "Imperium" (Imperial Rome).
Some of the attributes for governments can be altered at the top of rules.txt. These are:
-Unit support for cities under Monarchy (def:3)
-Ditto for Communism (def:3)
-Ditto for Fundamentalism (def:10)
-How much science is lost under Fund.
-Communism equal to what Castle distance (def:0). Distance of 0 equals no corruption.
-Max effective science rate in fundamentalism
With this you can make some changes to you governments. I don't know if it is possible to make more in-debth changes...
Arius