Perhaps a member of Akatsuki is in the organization to learn their plans and bring them down from the inside...perhaps Tobi or Itachi. I was just thinking that from the flashbacks to Itachi's relationship with Sasuke, he got more and more distant from his as time went on. What if Itachi became a disciple of Danzou...who wiped out all of his emotions and convinced him that Akatsuki was such a threat that he must join and in order to gain their trust he must do something extremely dispicable like killing his entire clan. Or perhaps he knew that the Uchiha clan had the ability to suppress or control the Biju chakras and felt it necessary to wipe out that ability. Why else would he wipe out the entire clan? To test his abilities he could have just killed a few of the best members, but he killed all of them..unfortunately for Itaichi he couldn't bring himself to kill his little brother and left behind someone who would come after him and someone who could suppress or control the Biju chakra. Then Danzou saw that Sasuke had escaped Konoha and was becoming stronger and with Orochimaru's help may be able to kill Itachi and derail his plans to bring down Akatsuki from the inside, thus he had to send Sai to kill Sasuke...why else would Danzou be so intent on killing Sasuke instead of worrying about Orochimaru? Maybe this theory belongs in the wacky far out or some sort of fan fic thread...but some things that have happened don't seem to make too much sense.