Ok, so call me a conspiracy theorist, but I have two things to say that I have noticed so far that seem to make sense to me.
First, Karin. I have a theory about her and Oro. If Oro did manage to get the Sharingan, he'd only have it for a few years, right? Well, that won't do him much good. What if his intention was to 'breed' using Sasukes body with another person with a unique bloodline, like, say Karin, who "appears" to have the ability to sense chakra. What better combo for a body to later inhabit than someone who can sense chakra AND copy techniques. So maybe that's partially the cause of her obsession, as Oro put her in charge of that lab and told her she was gonna basically be the mother of SasuOro kids.
Second, Sai. His sensai, more specifically. What if Sai's sensai was Shikamaru's father. Going back to the manga where he was packing up his ninja gear for the mission with team Kakashi, a guy with a ponytail SUSPICIOUSLY like Shika's dad only in an ANBU outfit shows up and lectures him about 'Roots,' his emotions, etc. What if that is indeed Shikamaru's father, and he's been in roots the whole time. Could help to explain why he's drinking, and usually seems pretty depressed. Like when Chouji was in the hospital after the Sasuke rescue mission his old man gave him that speech about leading a team etc, seemed about as preachy as Sai's sensai, in the later manga. I dunno, call me crazy. I don't have links to pic's of the Sensai and Shika's old man, if I did I would post em to support my theory. If anyone agrees it IS possible and have pics, please, by all means, post em.'