First time posting here so go easy on me, I love the site and you all do great job with theories. Ok here goes....
I think we basically saw Jacob win when Juliet detonated the Jughead. He knew exactly what MIB had planned and instead of fighting it he literally sent Jack n co back to create a new reality so MIB doesn't win. I don't think MIB is bad at all, I think he is just tired of playing Jacobs game.
Not sure how it will get there exactly but I can now totally see the series ending with the opening pilot shot. I think alt Jack will have to die or something to return to the original timeline that we all know but this time when he wakes up in the bamboo he will realize his fate is on the island and will know what not to do this time. Possibly playing MIB to Locke's Jacob but I'm not going there right now.
One more thing and I'm stealing it from Fringe- Little Ben was killed by Sayid but Richard-who can possibly travel between realities brought back alt Ben-which is why his innocence was lost and wouldn't remember anything.