Just a curious thought to amuse myself:
What if Jacob is Aaron Littleton and the Man in Black is David Shepherd? Two cousins displaced in time and space? In the original timeline, David doesn't exist. What if, in the flashsideways, Aaron is never born? Claire looses the baby in childbirth.
And so, Jacob and the Man-in-Black are then fighting each other for the right to exist. Each of them is working to try to actualize the timeline that allows them to exist. This would give a whole new meaning to why Boone, in Locke's vision told Locke that he was "here to help you find your way again, so you can bring the family back together."
I have no evidence for this, it's just a random thought that I felt like sharing.