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Who is leading the Others?
This one is hard to prove but I believe it is true. I believe that Jacob /never/ led the Others. It was /always/ McLoophole. Here is how I think it went down:
1) Jacob and McLoophole are on the beach and they see Richard's boat. Jacob makes a speech about having faith in humanity, and McLoophole thinks we are all apes who can't get along. Almost as if it's a contest between the two of them to see if humanity decides to kill each other or not. McLoophole points out that every time people come to the island it results in the same thing, they attack and kill each other due to greed. Jacob says 'all it takes is once, it makes the previous failures nothing more than progress'. (quotes may not be exact but you get the idea)
2) This 'contest' if you will, is either a product of their own doing, or else it's the rules in which they are bound by in living on the island. Rules such as:
+Jacob cannot interfere or talk directly to the people on the island. The only exception is the first person he meets...but even this person cannot hear the whole story behind this 'contest' between the two of them.
+McLoophole can take the form of people who are dead on the island. But he cannot force or threaten them into doing anything. He is only allowed to manipulate. In the form of the black smoke, I believe he can read the minds of people he confronts.
+McLoophole is allowed to kill people. However, he doesn't want to because he needs people alive so that he can manipulate them. Killing people thwarts his purpose of proving to Jacob that people will kill each other. An example of this is when Eko dies, Eko doesn't listen to the ghost of his brother and thus is non-manipulateable (expendable).
+Jacob has to stay in 'the shadow of the statue'. He's kind of in a 'time-out' until the contest is over.
+McLoophole has to stay in the Temple. However, he is allowed to wander the island in the form of dead people.
3) Jacob meets Richard, gives him the ability to not age...he needs Richard alive for the course of this contest. Jacob warns him not to listen to ghosts of dead people on the island, and tells him the same thing he told Ben at the end: "you are free to make your own choices", or something like that. Says never to visit him directly unless summoned (otherwise it could violate the 'contest' rules).
4) from then on, McLoophole is using Richard, Widmore, Ben, and every other leader of the Others. Those "lists" are coming from McLoophole. We don’t know how or who, but once the first person dies on the island McLoophole begins using ghosts to toy with people. The ultimate goal of course is to use one of these people to kill Jacob, but the other goal is to promote greed and to get them to kill each other.
Consider that Ben never saw or spoke to Jacob, and consider what the Others have been up to...for example building that runway (Sawyer and Kate in the chain gang). The runway was needed for McLoophole's final manipulation--the landing of flight 316 where he can take the form of Locke.
The unfortunate thing is that it appears that Jacob lost the contest, since Ben killed him at the end of last season. However, there is the bomb and the chance that time has changed due to that explosion.
The only 'move' Jacob seemed to make was to reach out to specific people in his flashbacks, he seems to /touch/ each one, even to the point where the camera pauses: he visited Kate shoplifting, Sun and Jin's wedding, Jack on the hospital, Locke just after falling out of the building, and Sawyer as a grieving kid, Sayid before his girlfriend was hit by a car, and Hurley after leaving prison. All of these people were involved with exploding that bomb and possibly changing time.
Getting off topic for a second...Sawyer was the only one who was touched but was not on flight 316. It could be because Sawyer almost made it off the island (he jumped off the helicopter in a selfless act), or it could be because Sawyer provided a 'link' to the rest of them...guiding them to the correct time (1977). And one note about Sun. Jacob sort of reaches out toward Sun and Jin to touch both of them at the same time, and we can see Jin being touched but not Sun. It's possible that he never actually touched her, which explains why she didn't jump back to 1977.
My key point with this theory is that the writers gave us a twist...Jacob /never/ led the others. Ever.