I think scrambling and the AA rule changes are my favorite. The rule keeping airforces from scrambling off anything that wasnt an island contained in a single sea zone was a hold over from the old pacific game, the first one to ever use naval or air bases, when all of these bases were only on islands to beging with. It needed to change and has added so much more to game play.
Having AA be its own unit really needed to happen. With all the new facilities and bases comming with their own self-contained AA, there really wasnt much point to independent AA as its primary function in previous games had been to protect ICs. Its neat, keeps the simplified old rule for AA for facilities and bases defense, and adds a component of AA to standing armies.