The biggest complaint I've heard is they took away the "MY" buttons on the 2k5 remote. Now you have to drill through menus to get to your pictures, movies, music, etc....
But the greatest advantage of the new remote is that it supports learning where the old one didn't. So you can use it to control the volume/power on your TV... very helpful in minimizing the shuffling between two remotes to control playback/transport functions and volume.