I have found using the BI.exe the AI does a lot of naval invasions, too much in my opinion. I went back to the RTW.exe as I got sick of Carthage and the Greeks sending boatload after boatload of one and two unit armies to Italy. I also found the AI to be slightly more aggressive which I did like.
Most people seem to like the changes the BI.exe makes, though, so its all about personal preferences.