I'm also asking myself: which one was the best compared to the original and its modding possibilites? (So, not only as absolute value: is it bigger the step from civ3 to RoC or from Civ4 to RFC?).
My opinion on Pros and Cons (I'm not counting here the aspects that are present in both, such as terrain graphics or spread of resources):
+ 31 civs, including Israel and Austria
+ Loading times reduced to 95%
+ Religions added
+ Larger map
+ Random map
+ New tech tree
+ 2nd UU
+ Many new units and buildings
+ Ethnical unit graphics
+ Removal of any inaccuracy of the original game
= All the additions made through little tricks (such as invisible resources) because Civ3 was semi-hardcoded
- AI settling in weird places
- Barbarians present only at the beginning (once killed, they wouldn't appear again)
- Civs all alive at the beginning of the game
+ Different start years
+ UPs
+ UHVs
+ Stability and collapses
+ Congresses
+ Plague
+ City naming system
+ Scripted barbarian attacks
+ Unique settlers AI
+ Independent and minor civs
= All the additions made by writing code thanks to Civ4 flexibility
- Smaller map but similar loading times
- No random map
- Almost no new units, buildings and techs