I have no strong evidence that support this at all....i repeat this theory has no substantial evidence at all as to why i think that the man in black is jacobs father.
Why i think that well the way they interacted with one another so polite and dignified for someone who wanted to kill the other, it seems like the sons views clash with his fathers idea's of the world. Plus one is signifigantly older then the other
Both Damon Lindelof and J.J. Abrams are huge star wars fans and already this season we have seen reference to"empire strikes back" in the episode "some like it hoth". well dosn't anybody know how empire ends with those words"luke i am your father....come with me to the darkside(I.E blackshirt)and we can rule the galaxy as father and son. thats about all i got to support it.
But then you ask why would dad want to kill son..could it be clashing views, change of the world from jacob leading to a different outcome?..who knows...all i know is that the father wants him dead but can't do it himself..maybe theirs a rule saying you can't kill family members on the island idk..maybe Jacobs death would lead to positive change in the world and jacob just dosn't want to die he's enjoying his time on the island and thinks it will all work out with him around.
P.S. remember the brain washing room in season 3 that karl was kept in so a saying comes on the screen"God loves, as he loved jacob" hmmmm.are they angles? demons? saints? higher beings? well were just gunna have to wait and see