My short Theory on MIB ("One of these days, sooner or later, WE'RE gonna find a loophole")
This is not a very in-depth theory, but I believe it could a crucial clue.
When MIB is talking to Jacob on the beach, I firmly believe that he says "WE'RE going to find a loophole" (Listen VERY closely).
I believe that this implies that MIB is part of a group of people that want Jacob dead. I have no idea whether or not MIB is simply the smoke monster, just manifesting as some guy who had been killed on the island (One of the Hansos?) Either way, I think that whoever or whatever MIB is, he already has his "army" against Jacob, and I believe that John Locke ties into this somehow.
Another point I wanted to make, is that at the end of season 4 when Ben moves the island, John Locke, Sawyer, Juliet, Faraday, etc. "move" along with the island to whatever year their first "flash" went to. I think Faraday knew exactly what was going on the entire time, but more importantly, I caught something very key I think: When Locke flashes the first time, and Richard and the Others VANISH, Locke encounters Richard later when they were in 2007 and Locke angrily told Richard that they "disappeared" when the island moved, and Richard snapped back "I didn't go anywhere John, YOU DID." Does this mean that when Ben moved the island, WHAT HAPPENED IN THE NEXT THREE YEARS????????? Things didn't just freeze. Locke, Sawyer, Juliet, Faraday, Miles, Rose, Bernard - THEY are the ones that disappeared, not The Island or the Others. So what happened when all of those people got sent back to 1977? What happened in the current time ON the island???
I believe that somehow, some way, John Locke is not truly dead. I have no idea if it's an alternate timeline, being reserrected, whatever, but I just don't think that LOST would end John Locke's story the way it seemingly ended in season 5. There's just so much we don't know yet, and I strongly believe that the real Locke is the one that made Ben kill Jacob. I believe that this ties into MIB - I think MIB is just someone or something that Locke is on the same side as, as well as a bunch of other people (The people in the Temple???), and for some reason, they want Jacob dead. I think the major twist might be that Jacob is really the "bad" one, and "The Others" have been evil all along somehow, and it will be up to Jack and Locke to ultimately work together to save the world somehow... I'm done!