I'm a longtime lurker and have really enjoyed reading these theories. I had some thoughts and figured I'd better get them on here before they can be disproven later tonight or Sunday. Here goes:
I think that ATS showed us the Smoke Monster is no more MIB than he is Locke, Christian, Ecko's brother or anyone else whose form it has taken. The evidence is the bodies. ATS gave us the final piece to figure this out. Let's look at a partial list of people most could reasonably agree the Smoke Monster has inhabited/mimicked:
Christian - coffin deposited on island, body missing but was certainly dead before coming to the island.
Yemi, Ecko's brother - dead on the plane with the St. Marys
Locke - dead and buried at the cemetary on the beach
and finally . . .
MIB - dead and lying in the caves with his mother
So what makes MIB and his backstory stand out beyond these others to the point where FLocke is pretending to be 100% MIB? I believe it is merely that the smoke monster and MIB have/had the same goal: to leave the island.
Others here have made a strong case that "Mother" was also the smoke monster by evidence of the destruction of the camp, her knowledge of what happens when one enters the light, and her sudden appearance in the well. While I'm not 100% sure she was the smoke monster I do tend to think that the story told in ATS is not the beginning of the story, but a loop in the cycle. Meaning, the smoke monster already existed before ATS either as Mother or its own entity (Let's also remember that before the Romans came the Egyptians and there is clear evidence that the smoke monster was around in the Egyptian markings under the temple).
Let me slide into my other theory here: Jacob's motivation. We saw in ATS how Jacob was pulled into his role, or quite literally forced into it by his "mother" who actually said, "You don't have a choice." Mother has actively manipulated him and his brother since birth to act in an orchestrated series of events that led to one son taking the mantle of island protector and the other providing a release from her imortality. Now, I don't think it happened the way she planned, but both events occurred, and you could tell that both events pleased her.
Jacob goes too far in his rage, and sends MIB to a fate worse than death by sending him into the light. There, the smoke monster "took his body" and is using his personification to actively manipulate Jacob, who we know is now the one making all the rules.
Who better to manipulate Jacob than his own brother? Since MIB and the smoke monster have/had the same goal the scheme carries more weight with Jacob and the audience, but thankfully Jacob is not buying it. Because his motivation is to handle things totally different than Mother did.
Mother took them from birth, controlled their environment, shaped their outlook on life as best she could. Jacob watches from the lighthouse upon his candidates, intervenes much more minimally than Mother ever did, and lets the candidates come to their own conclusions.
Mother - "You don't really have a choice."
Jacob - "I want you to know that you have a choice."
Now that Jacob is making the rules, he is engaged in a game with the smoke monster, who is either pretending to be his brother or at best only partially his brother - never forgetting that HE LAID HIS BROTHER TO REST IN THE CAVES long ago. He is setting up an ending much different than the one Mother tried to orchestrate - one that will finally end all the loops, and though I haven't figured that out yet, I love to read here and see what else you guys can come up with.