New plugin integration method means that all existing plugin 'bridge' modules for Drupal have to be updated.
Configuration settings have been rearranged, so any custom configuration being set via a module has to be adjusted.
The highly convenient 'Styles' drop-down no longer exists, as CKEditor developers expect you to write your own plugin for custom styles that does proper sanity checking.
Workarounds? There are some, and we'll explore them.