First of all, I'd like to see Mythic Dungeons introduced in the future (although Blizzard currently has no plans for them yet). One of the things that set's heroics aside from normals is that the heroics bring new phases, resistances, and abilities to the boss fights and mobs, and completing them induces a sense of accomplishment. Mythic dungeons could perhaps expand upon that by making some mobs completely immune to a certain type of damage (ie, fire elementals immune to all fire damage), make fights with ghosts require a certain spell, and make boss encounters more challenging and unique.
Speaking of challenges, I think there should also be a challenge raid setting too. Basically same thing as the dungeons but with raids. They'd have different rewards, ofcourse.
I think levels should have bonus objectives. We already have achievements, but bonus objectives would make dungeons and raids a lot more meaningful and entertaining. Perhaps a certain way to defeat a boss, using a different path, a timed run, etc.
Finally, I liked how Timeless Isle had treasure chests. Maybe sprinkling them across not just the game world but the instances too would be cool!