As the version numbers increase, the climate simulation gets better and the basic terrain type generator probably, on average, gives better results too (the ocean/land/hills/peaks generation). The order of development was PW -> PW2f -> PM3.1. Some people like the various peculiarities from the earlier map scripts, so they are still useful.
The C2C Perfect Mongoose 3.1 is modified beyond the regular PM 3.1. Most (or all) of the changes AIAndy made to it are now in the regular PM 3.2 mapscript and represent most of the changes between the regular PM 3.1 and 3.2. So C2C PM 3.1 is mostly a match for regular PM 3.2, plus it has the river and resource quantity options (which are not in regular PM 3.2, or 3.1 for that matter) although C2C's does not have the option of using the weird climate generation system from regular 3.1 (regular 3.2 has this option) which was actually hexagonal in nature (it was adapted from one made for Civ5 and it only considered 6 of the neighboring plots instead of all 8).