Okay - I've done alot of commenting on this subject lately, and it has become quite the difficult task adding my very detailed theory to each blog that I see, so I decided to create my own theory to see what everyone else thinks.
Firstly, I'm going to argue that MiB and the Smoke Monster are not the same. I am not going to argue against theories that say that they ARE the same because, quite frankly, there really isn't enough evidence at this time to point either way... at least I don't think so. In order to start my theory, I'm actually going to begin it with another thoery, which details what the relationship between Jacob and MiB are, so here we go:
I believe that "the war," or "the game," that is being played by Jacob and MiB centers around the question of whether humans are born inherently good, or inherently bad. We know from the opening scene in The Incident that this game has been going on for some time, and Jacob seems to have been "proven right" every time thus far. As we all know, MiB is looking for a loophole to kill Jacob and possibily dispel his belief system. We then see Jacob off island, "recruiting" several of the Losties, and it appears that he has the ability to pre-determine their fates, in the sense that he makes them come to the island. I believe that these people are thought to be "good" people by Jacob. Consequently, the rules, as I believe them to be, dictate that MiB can only kill Jacob by proving him wrong with regards to his theory about people being inherently good. To do so, he can use whatever means possible to manipulate those whom Jacob brings to the island. MiB needs to use one of the people that Jacob brings to the island to kill Jacob. However, up to this point, MiB has not been successful in doing this.
On to Part 2...We know that several people who we believe to be dead have been re-animated in some way. The people who fit into this category are Christian, Yemi, and Locke. Claire is not confirmed dead or alive, although in Season 4, she certainly appeared to have a calmer, all-knowing attitude about her much like Christian. However, I'm not going to include her in this. Christian and Yemi's re-animations are similar because their dead bodies disappeared as soon as we begin to see them "living" again. However, when we see "Flocke," it is very clear that Locke's dead body remains intact and in plain sight for everyone to see.
Part 3. Someone has been living in the cabin. Some people believe that it was Jacob, some say MiB. For the sake of my theory, I choose MiB. When Ilana and co. arrive at the cabin in Season 5, she examines the inside, and informs everyone else that, "He's not here, Someone has been using the cabin." (that is not an exact quote, but close I believe). Because it is clear that she is on Jacob's side, I believe that quote indicates that someone ELSE was living in the cabin. Also, I assume that the ash circle around the cabin was used to KEEP THE INHABITANT INSIDE, rather than keeping outsiders out. Each visit made to the cabin, whether it be Hurley, or Locke, we are given some type of clue that SOMEONE is inside. However, when Ilana arrives, there is no one there, and she comments that the ash circle has been broken. I know that it is a little bit of assuming, but I am thinking that this means that someone compromised the circle so that MiB could get out.
Part 4. It has been suspected that the smoke monster is responsible for re-animating some dead bodies. We have also seen the monster influence a character's judgement and thought-process. We definitely saw the monster manifest itself as Alex to convince Ben to follow Flocke. We also have assumed that the Monster manifested itself as Yemi to toy with Eko. I believe that the Monster actually brings the original dead body back to life, in a somewhat different state of being. The characters that have been brought to life act differently than than when they were actually alive. However, there is something a little different about Flocke. He seems to be a bit more "concrete" and human, wheras Christian and Yemi appear to be more like spirits, for lack of a better term.
My theory here is that MiB and the Smoke Monster are seperate entities yet connected. I believe that MiB, for one reason or another, has been confined to "Jacob's Cabin." Whether he was imprisoned, tricked, or it's just part of "the game," I believe that the ash circle keeps him from moving outside of the cabin. I think that the smoke monster is an extension of MiB. It possibly serves his will, and I think that it is recruiting for MiB's side in the war, as well as attempting to kill off individuals that it determines cannot be truly "turned" from Jacob's good side. I believe that is why Seth Norris, the pilot was killed. Frank was supposed to be the pilot, and he is obviously a candidate for something with Jacob. I think the monster was trying to eliminate Frank, because it knows that Frank cannot be influenced to change sides. I think that Eko was initially spared because when the monster "judged" him, it saw that Eko might have a sinister side to him. However, later on, when he refused to repent to "Yemi," the monster knew that Eko's decisions are based on protecting those he cares about, and not out of an evil quality about his personality. I think this is why the monster killed him, because he did not want Eko on Jacob's side for "the war."
Back to my point in Part 3 above. As soon as we learn that the ash circle has been broken, we also experience the first dead body that has been "re-animated" in a way that still allows the original dead body to remain intact somewhere on the island. I am of course speaking about Locke/Flocke. Unlike Christian and Yemi, Locke's body remains in the casket for others to see while Flocke is roaming about on the island. I believe that this, coupled with the fact that we just learned that the ash circle was broken, could be evidence that MiB escaped from the cabin and was responsible for taking the form of Locke, and that Flocke is not similar to Christian and Yemi, who I believe were brought back by the Smoke Monster. I'm not really sure what any of this means in the big picture, but this theory is really just a bunch of observances that I have made.
I'd love to know what everyone thinks, and I'd love even more for someone to elaborate and help me develop this further!!! Hope you all enjoyed this!