I have just finished re-watching the 5th season of lost and I have some new thoughts on both Jacob and MIB. The question of the origins is a mystery, but there is one thing that is clear to me and that is that Jacob and MIB are both evil. I know that there have been articles written on here discussing who is evil and who is good and that there is no clear line between them, or that there is neither good or evil but there is.
Though out the series many characters have stated they are the good ones, Ben said it to Michael in season two, and Bram said it to Frank in "The Incident". Jacob has been described as someone that believes in free will which is showed in "The Incident" when he tells Hugo that the choice is his on whether to get on the plane and to Ben when he tells him that he has a choice, but that is not that case. Remember when Sawyer states what a con is, you make a person think that something is their idea but it is really yours, you just make them think it is. Same thing Jacob did with Hugo, he just made Hurley think it was his choice to get on the plane but it was not.
Jacob and the MIB do not care about free will because of their game that they are playing with each other and they both got their players, Jacob got Jack, Kate, etc and MIB got John and Ben and they both forced their players into this game. Neither of players know they are part of the game and they are all there against their free will. This is showed in the opening scene of 'The Incident'. When MIB tells Jacob that it was him that brought the ship to the island. That is Jacob violating free will. Look at what he says "it only ends once. Anything that happens before is just progress". In other words I have brought different people to the island at different times, against their free will, –they all have died and I don't care.
So in conclusion both Jacob and MIB are evil and that is why in my opinion that Jack is going to lead all the survivors against both Jacob and MIB. The island is itself a individual entity and the worst thing that happen to the island is Jacob and MIB. I think that the island wants to get rid of both of them and that is what the survivors of 815 is going to do. I think Jack, Sawyer, etc are going to kill both Jacob and MIB and the reason is because of their little game they are playing with each other that has cost the lives of so many.