I'm going to share my theory, which is more of a "big-picture" theory versus trying to explain details - as I think Lost will end with many details unanswered but (hopefully) we understand the big-picture.
Let's assume the whole thing is similar to this game of Backgammon that Locke shared with Walt in season 1. Let's also assume that the two sides are Fate (MIB) versus Free-Will (Jacob).
Basically, backgammon is a game between 2 players that could be traced to ancient Egypt. In the game, you roll the dice (fate) and then use strategy to make a move (free-will). Interestingly, the pieces can be called "men" and to win the game you remove all the pieces from the board. The playing time for each game is short, so usually you play several games called a match.
This draws obvious parallels to Lost. I theorize it's a game between MIB and Jacob to determine whether fate or free-will will win out. Jacob continues the game, "making progress" each time but it ends once (whoever wins the match).
Let's take the analogy further. In backgammon, no 2 pieces can occupy the same space simultaneously BUT if a player's piece is "hit" by the opponent by landing in the same space that piece goes to the bar in the middle of the board. That piece must then re-enter the game on the opponent's home board and that player cannot play until they do. To win, a player must move all his pieces to his "homeboard" and he can then remove the pieces from the board.
We know that Jacob is the one bringing people to the island, or instigating these games ("I was brought here like everyone else" -Dogen). In Lost, he has done this by influence but it has always been their free-will. He has brought the Others as pieces and those not on this list are killed because they don't matter in the end. MIB has grown tired of these games, so Jacob has chosen his last set of people to bring - certain Losties who are essential to winning.
However, the MIB knows that one of these people are different from the rest - he does not want to leave the island (Locke). Locke is also a man who believes in fate. Locke continues trying to convince people their fate is on the island and tries to deny them the free-will to leave. Even the submarine, which Ben said was so that his people knew they had the choice to leave, was destroyed by Locke. Locke tries to thwart people from leaving when Widmore's freighter comes. And he actually leaves the island to bring people back. Notice, the people that influence Locke to do these things don't give him a choice. Locke MUST do it because he is "special." Anyone on the side of MIB/fate, such as Widmore, Christian Shepard, Eloise are on the side of fate. Locke goes to the O6 off-island and says they must come back, it doesn't work, so he kills himself as he thinks he MUST do...the loophole that MIB needed to win Locke to his team.
In backgammon, there is a doubling cube that can be used to quicken the game and the stakes. There is even a "Jacoby Rule" that allows a player who is behind to double, thereby bringing about a quicker conclusion. I believe that significant island events are probably akin to this (blowing up the hatch, Widmore's ship giving them an option to leave, the island moving, the Incident).
Desmond is special because the rules don't apply to him. In S3 when he went to this other timeline, he was at a pivotal point in the ring shop. He freely chose to buy the ring, but Eloise tried to stop him. He eventually went with what he thought was fate and *poof* went back to the "main" timeline. He tried to stop Charlie from dying, which he could have but he and Charlie eventually resigned to the belief that it was fate for Charlie to die.
The ATL is another game being played in their series of games, but Jacob is dead (lost his influence?) and we are seeing the result of that. The island (the gameboard) is sunk. But we continually see the Losties make pivotal choices (free-will). Jack's dad's body is gone again (hmm, no closure for Jack...will he still end up drunk and drugged). Kate decides to go help Claire, rather than keep running. Claire chooses to go with Kate and keep the baby ("If you want, you can have your baby now"). Sun is given the choice of whether to save Jin or not.
As the rules of backgammon dictate, the players can't be removed from the board until they are all in the player's home. I think "dead Jacob" was MIB because Hurley was not given a choice to go to the Temple for Sayid. Plus MIB obviously knew the way in the Temple was underground and that is where Smokey killed Rousseau's party. This might not mean Sayid is good or bad, but he is back in play like he needs to be for one side to win (he is now "claimed"). Interesting the Others aren't that worried about Sayid as they are Smokey. MIB must bring all these particular players back to his "home" to win. He will convince them it is their destiny/fate.
I don't know if "winning" means they all die or they all leave the island, but I believe it's an outcome they must all share. The ATL exists because, I believe, we will see them all make free choices to determine their destinies and this means Jacob will win. Either way, this puts Jack in a critical position since he is regarded as the "free-will" guy.
There are probably many holes and this theory doesn't explain everything, so please let me know what you think. I view the theory forum as a collaboration. The great thing about Lost is we are so close to the end, but there are still so many ways this could go (like backgammon and free-will!).