Several posters at the Fuselage have mentioned that in the Bible, Jacob has a son called Benjamin. Could that be the relationship between the show's Benjamin Linus and Jacob? Sounds nuts, but it made me think of something that has always bugged me about The Others. When Locke was going to become leader, he had to kill his dad first. They even brought his dad all the way from the mainland to the island so he could do it. So, it seems that to become leader of The Others you first have to kill your father: horrific right?
We saw Ben kill Roger in the Purge. But it's intriguing to speculate: what if Roger wasn't his dad? What if Jacob was his father? What if this is Jacob's loophole: he is killed but at the same time Ben becomes the true leader of the Others because he has now, finally, killed his real father? Maybe this has something to do with Ben being saved by Alpert/The Others when he was a child: whatever happened then may mean that even if Jacob wasn't his biological father, he is his "real" father somehow?
Ben never got to see Jacob before, because he hadn't fulfilled the requirements of leadership. It would make the scene with Jacob at the end of the finale really poignant in a way: Ben meets his father for the first time and kills him.
Not sure I even want this theory to be true, but I can't help thinking about it. The requirement to kill your father always seemed so harsh and barbaric to me. And whether Jacob is Ben's father, the scene when Ben kills them was in many ways a patricide regardless: Ben had followed this "invisible father" for so long, and their confrontation was in many ways like a confrontation between a father and son.