Jack is the new Jacob. As we have seen in S06E04 "The Substitute", for many years Jacob has been searching for a candidate, to replace him as the protector of the island. In the cave we've seen some names (like Jones from the US Army) and (Jack) Shephard is one of them. Well, I think eventually he'll be the one who replaces Jacob.
Why? Because Jack wants to fix things. From the day the 815-people crashed on the island Jack wanted to fix them and to get them off the island. When he was off the island, he wanted to go back to fix everything. When he could drop a bomb to make sure nothing of this happened, he wanted to do that. Jack just wants to fix things. And becoming the new Jacob is his ultimate fix.
Matthew Fox once said he, and the producers, know how the final scene of LOST will look like.
And just watch this vid, when Matthew is talking about S06E04 and 'candidates'
"I have no idea, obviously, who's gonna ultimately be the candidate, or who's gonna be the chosen one, or who's gonna make it to the end, but... I'm really curious to find out."
If you look from 0:32 till the end, you can see a very subtile smile on Matthews face. And he's even looking down when he says 'really curious'. Is he? I think he knows more. For a reason... Jack is the new Jacob.
And what about Jack in the ALT, you say? Well, I think the 'flash sideways' show us what's happening after the end of season six. There will be some kind of reset, the 815 people will be back on the plane while not knowing what happened, and Jack will take care of them, fix things again so they're doing fine. Jack fixed Charlie, he will fix Jacob. And when everyone is doing fine again, Jack will go back to the island and live happily ever after as the new Jacob.