the choice to combine or not combine your library with the B&N library
support for Calibre's tags system for organization
ability to delete from the device
better dictionary integration
choice of dictionary - the Webster's pocket is pathetic
cover as screensaver
ability to reverse the page forward/back buttons in settings
ability to re-order and hide icons on the main menu
and any little tweaks that might improve battery life
I know some of these are available through soft-rooting, but I'd rather not.