I believe that MIB is truly Christian Shepherd and has been all along. There is no way of knowing whether or not I am right or wrong, but I believe there are some good hints that indicate I definitely could be correct.
#1. The actor Titus Welliver, who plays "MIB" in the opening scene of "The Incident", looks like a younger version of Christian Shepherd. Obviously, most people believe that it was the Black Rock sailing towards the shore in that scene of MIB and Jacob, which would mean that this was way before Christian Shepherd's lifetime, but #1. It might not have been - it could be the 1900's, #2. Even if it was back then, Jacob and Richard do not age, which means that MIB might not either... maybe Christian lived on the island for hundreds of years and finally left when he still looked like Titus Welliver (In his late 30's/40's?) Maybe his father Ray was in on this plot too somehow, because perhaps Christian realized "the loophole" might be leaving the Island and having children to use as "pieces" to defeat Jacob. So it's very possible that the "Titus Welliver" Christian may have left the island and ONLY THEN started to age. #3. Titus Welliver looks a lot like a younger John Terry, and ! also sounds a lot like him as well... just saying....
#2. After 815 crashes, Jack finds Christian's coffin empty, which means that INSTEAD of LOCKE's instance in which his body was never actually "possessed", that Christian awoke from the dead (MY THEORY) upon crashing on the Island and "returning" to the place where he had ETERNAL LIFE, thus ressurecting him. Either that or The Smoke Monster took possesion of his body, but who is to say that the Smoke Monster itself isn't Christian/MIB???? I think that when the plane crashed, MIB (Christian) returned to life and perhaps this had been his plan all along in order to take over the island. I am not going to get into the alternate realities and time travel in this post, but I strongly believe that Christian was always MIB and left the island and knew the only way to come back was to be dead for some reason, and he knew Claire and Jack would be on that flight somehow, and purposely killed himself when he did because he wanted Jack, Claire, and maybe the rest of that specific flight ! of people on the island for a reason we probably still don't know.
#3. To me it seems very clear that Ben was working for Jacob the entire time along with Ilana, Bram, and the Others (except for Richard, who I believe to be one of the main bad guys who's true nature will be shockingly revealed in season 6). They all wanted the 815ers to create "the incident" for an unknown reason. Think about it - Ben convinces Jack and Sun to return to the island. Jacob convinces Hurley to return. Jacob and Ilana are allies obviously, and Ilana forces Sayid to return. Connect all the dots, and its clear that Ben is the one conning everyone here - Jacob WANTED Locke and Ben to kill him, for a reason I do not yet know. Ben was in on it, and I do not yet know if Locke is or isn't (I believe "Flocke" to be the true Locke, read my other posts to understand). The Others and Ilana/Bram's team are clearly all working for or attempting to help JACOB. They are the "good guys", or so it seems at this point.
What does this have anything to do with Christian "MIB" Shepherd? Because ever since the 815 crash, Christian has been popping up around the island very randomly, often trying to convince our characters to do something or not to do something. And the one thing I have noticed is that he HATES Ben. He tells Locke "I said YOU had to push the wheel John." And Locke responds "But Ben said bla bla bla" and Christian responds "And since when did listening to him ever get you anywhere worth a damn??" Ben is clearly trying to prevent MIB from doing something bad which if further evidenced by his relationship with Jacob that not many people realize.
Ben ONLY wanted Locke dead AFTER he had turned the wheel. WHY??? He could have killed Locke 4430434535 times on the Island but did not. Only AFTER he turned the wheel and ended up in Tunisia. I find this VERY interesting. After Locke hears the voice say "HELP ME" in the Cabin, Ben shoots him though... and after he does what CHRISTIAN tells him to (help him?), Ben finally kills Locke. Ben and Christian DO NOT like each other. Jacob and MIB do NOT like each other. Ben is Jacob's most trusted follower and may even be his son. I believe Christian to be MIB, you do the math.
#4. Christian takes Claire away before she can leave on the helicopter, but not Aaron. This means something. Christian wanted Aaron to be off island, but not Claire. It is said by Claire's mind-reader dude that something horrific will happen if Claire does not raise the baby. MIB seems to want to cause something horrific. Christian caused Aaron to go home without Claire. Coincidence???
#5. Christian is in the cabin, not Jacob. The Cabin is surrounded by black ash, which I believe was intended to keep Christian trapped in some way. Notice that before the ash circle around the Cabin was broken, on-island Christian didn't and maybe couldn't actually touch anyone or hold anything, and seemed more ghost like, but after the circle was broken, perhaps by Hugo, he was able to carry things (Aaron). I think he simply wanted Locke, or someone else, to break the circle of ashe so that he could become more than just a ghost, or something close to that.
#6. Christian wants Locke to die, because somehow he knows that if Locke dies, Jacob will end up being killed. MIB hates Jacob. He wants Jacob to be killed. Coincidence?
#7. Christian wants Claire's mom to die in the episode in which he tries to convince her to turn off her mother's life support. Why? Because she is the one the recieves Aaron from Claire. I think that due to the mystery surrounding HOW Carole Littleton made such a remarkable recovery is quite simply this: She didn't. After Claire crashed on the island, someone or something made sure that the real Carole Littleton was dead so that some sort of "imposter" could take over her form and take baby Aaron so that he's able to fulfill his "evil prophecy".
Feel free to add any more reasons that you believe what I do: Christian Shepherd is the Man In Black!