I think we have to wait and see how the story plays out a little more. His objectives and priorities dont seem to be set strait, seeing as how he wasted his mangyekou to have fun torturing Sasuke instead of using it on Jiraiya and running away w/ Naruto.

I was thinking perhaps he doesn't use his sharingan to the fullest extent because it hurts his eyes as Kakashi has said, but that still doesnt explain why he wastes his oppertunities on Sasuke.