The major changes are listed below.
MAJOR - Added a "Depose Antipope" Casus Belli - Added an "Antiking" faction. The leader usurps the liege's primary title, deposes the antipope and passes papal investiture. The Pope can be called into the resulting war. - Not possible to set up an antipope within 50 years of one being forcibly deposed - Fixed bug in Linux where the game became totally unplayable if you ALT TAB - Now possible to play in Ironman mode with the ruler designer and mods (but you won't get achievements) - Significantly reduced the amount of event-spawned troops across the board to better reflect the rebalanced levies - Fixed crash bug in the Mac launcher (Fix attempt did not work, sadly, so Mac Steam users still need to disable the Steam community overlay) - Fixed religion reformation crash
Full patch notes can be found on the Paradox forums.