Add this to the never ending theories about Lost, but I have one for this. I think Jacob has visited everyone who has ever come to the island (Well, maybe not everyone, but the significant ones and then they probably brought some insignificant people along with them). When the man in black asks Jacob who were the people in the ship they saw off the coast and how they found the island, he answered himself saying it was Jacob who brought them here. Then he talks about how they'll do the same as everyone, come, fight, corrupt, destroy. Jacob declares this as progress and that it only "ends" once.
What I think is happening here is that Jacob has brought all these people to the island, the black rock, the Dharma Initiative, Desmond, other possibly castaways and most importantly the Oceanic flight 815 survivors. He brings them to the island by visiting them at very significant points of their lives, and influencing there fate to come to the island. The only difference with the Oceanic 815 guys is that everyone before them that he has brought to the island was progress, but these castaways are going the lead the "end" that he talks about.
I am also thinking that Not!Locke is like Ghost Christian. The real Locke and Christian are dead, but Not!Locke and Ghost Christian are manifestations of the island. However, Ghost Christian speaks on behalf of Jacob and I think Not!Locke speaks or acts on behalf of the evil part of the island. Whoever the man in black was, he got to possess Locke, while Jacob got Christian.