One of the main issues that comes up for me concerning extended minecraft play is breaking up one's typical gameplay routine.
Now it's important in a game such as minecraft to set goals for yourself to accomplish, however sometimes those goals are longer term and it's those interim periods that can really seem pretty uneventful.
One thing I was thinking that minecraft could really benefit from is sporadic waves of attacking mobs.
Not similar to the nighttime hazards we currently experience, but a random and brief period in which during the day or the night, a sporadic wave of enemies will spawn in in the player's general area.
It might be an interesting way to break up the routines that most players seem to get stuck in while they're playing for extended periods of time.