One thing I've noticed is how few reviews have pointed how hugely improved the 5.1 is on the first two films, particularly in the music department. The older box had a very "Chace-esque" sound as if they just passed the mono stems through a stereoizer. This time however it sounds like the used...
Here's at least one oddball change, Coppola has decided to standardize the subtitle fonts over all three films. They all use the Godfather III font now as seen here: Godfather I old Godfather I new