Not sure if this has already been said but here goes. My theory relates to the season four episode where Ben breaks into Widmore's flat and tells him that he is going to kill Pennny. When Ben enter's and Charles wakes up he ask's Ben if he is going to kill him, which Ben replies "you know I can't do that". Now we know that Ben is the leader at this moment and Widmore was the leader before him, what if there is some kind of code along the lines of "No person may harm a leader, either past or present and take his or her place". This could be why Charles was exiled from the Island, it was the only way Ben could take command of the Others. What if Jacob was the leader of some Pre-Other group and the MIB was his number two who wanted to take command, possibly to put a stop to the endless cycle of people comming to the Island and it always ending the same way ect. ect. ENTER FAKE LOCKE AND THE LOOPHOLE.
Thanks for reading.