sorry if this has already been suggested.... but does anyone think its a three-way battle between MIB, Jacob and Widmore? Maybe at some point of time Jacob and MIB teamed up against the common enemy and then fell apart... Jacob's last words "They are coming" seems indicate Widmore. I feel he is the threat to the island; maybe Jacob and MIB at one point agreed that island needs protection against Widmore, then at a later point MIB felt island doesn't need protection and Jacob stopped him from leaving it since he felt the island needed protection. Finally MIB got fed up, and started scheming to get rid of Jacob to leave the island.
Sorry if someone has posted the exact same theory; i just thought of this as a possibilty, haven't plagiarized!! :D