This entire show has been set up in terms of dualities/opposites. A couple of examples are black/white, Bad Twin/Good Twin, Science/Faith, On the list/Not on the list, Good Guys/Bad Guys, Jacob/MIB, etc.
My theory is that the show will end with two candidates taking the place of Jacob and MIB. Candidates, afterall, take the place of predecessors. I think that both Jacob and MIB want the same thing. They both want to be done with the island. There seems to be three things that they can do. One, they do nothing and watch as history constantly repeats itself in different manifestations. Two, the candidates take their place and they are the ones who must now endure eternity living on the island, trying to find peace. Three, everyone dies. If everyone dies or the candidates take their place, then the ATL will become reality for Jacob and MIB and the MTL will be reality for the Losties. If Jacob and MIB are unsuccessful, they go through another loop and the Losties are the ones who end up with the ATL.
When Jacob says that they are coming to the MIB, I believe that he is referring to the next group of candidates. Jacob has been a man of faith, hoping for the right group of candidates to come along and take their throne. MIB has been a man of science, giving up on faith and believing that the only way to get rid of this curse is to kill everyone off so that the loops stop.
We have seen evidence of MIB's work. He had Jacob killed. Even though he was killed however, we still see he has a hand in what is going on. That is because MIB has not yet fully completed what needs to be done. All candidates and himself, must also die. If not, things start over.
We have seen evidence of Jacob's work. He has given all the candidates a gentle push in the right direction. He has manipulated almost all aspects of the island in order for his plan to play out, starting when the candidates were young.
We have also seen how the ATL has started playing out. History has corrected itself in tiny ways that play out no matter which timeline is correct. For example, Jack's scar and Jack saving Charlie. Seeing this ATL would lead us to believe that in the end, the Losties win out and are able to resume their lives in the ATL and when things play out on the island, they will finally remember everything and realize how they got to where they are. They are already starting to become clued into little things such as the scar and the bumpy plane ride. They will all be in Los Angeles, free to live their lives, friends forever.
Or, how I feel it will really play out is it ends with FLOCKE and one of the candidates left on the island to endure the loops. When MIB found his loophole, he didn't understand one thing. Now that he is in Locke's body, he will not be going home to his ATL when Jacob's plan unfolds. Because Locke is a candidate, MIB will remain on the island in Locke's body, destined to live through the loops, living on the island next to Jack, who becomes a man of faith (sometimes a man just needs to look out into the water) to Locke's man of science.