Microsoft hasnt really done anything yet, seeing as all they did is buy it- not create anything themselves. Jeb and the team still make the game. But yeah, it's become different.
Some Nether blocks, new hostile mobs that look like zombies and skeletons, cat spawn egg (though I don't know if it was added in 1.9) and possibly some other stuff I can't remember. You can check it with the snapshot.