I really only want to put out this theory to say a few things... this isn't a serious attempt at figuring out anything, but I would like to share these ideas.
There was another theory dealing with water, and the light reacting to the water to create "smoke", thus the monster. I think that theory is wrong. The black smoke is merely Samuel's (The Man in Black's) soul, since that is all he has left. He can take another man's body and voice, but he will always have his soul/light.
I thought that Jack putting the light back into the island would make his own "smoke form", and detach his soul from his body (the body goes into that water outlet, on the rocks). Perhaps Jack's "smoke form" would have been white smoke, with lightning-like electricity pulsating through. Who knows, that's not what i'm getting at.
Samuel's soul was black. That is my problem. The writers have made him this horribly evil figure, though his background really says nothing to make him all to horrible. His motivations can be countered, can be sympathized with. He wanted to get off this island that he was forced to live on. So at the end of this series, the island "turns off" and he becomes mortal. He has John Locke's body, and I think the writers should have let him leave. He was mortal, he wouldn't have set anything catastrophic upon the world (there is nothing that says it would have been the end of the world, only what our cast-aways believed, and they believed Jacob to be the all-encompassing Good Deity)...
The writers made this tragic character evil, though it would have been much more sane for Samuel to have sat them all down and say, "Just unplug it, let me leave, and the island is all yours". Rather, they pretended he was evil just to set up that big finale.
Don't get me wrong, I love the way the Island-Timeline ended (not a fan of the Alt-timeline), but the more I think about it, the more the writers wrote themselves into a corner.