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Just thinking out loud here, but does anyone think there is a chance that MiB and Jacob are sort of in this thing together? Maybe it is a game like people have been saying, but that doesn't mean they don't want the same things. Both Jacob and MiB might both want the game to end, but in order for it to end, somebody needs to win. They will lie and manipulate and kill in order to do, so because they are men and don't want to lose (us men can relate to that, right?). This would also explain the theory that niether is good or bad. They are just simply on different sides/teams. So even though they seem to have completely different agendas, they are just using different strategies to win the game.
The bigger question would then be who is running this game, and why. Which brings it back to all the religious themes in LOST, the question of "why are we here". Not an easy answer to come up with.