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So I have a new thought that I haven't read yet. My new thought is in the second paragraph, but I want to explain how I came upon this theory first....
Clearly Locke's body has been somehow taken over by the guy from the beginning of the finale (dressed in black and talking to Jacob). We know this because at the beginning of the finale he says to Jacob - "Do you know how badly I want to kill you? And all I have to wait for is a loop hole." Subsequently at the end of the episode, Jacob says to Locke (just after we realize that Locke is still actually dead) - "I see you have found a loop hole".
Here is my new thought. Would anyone else find it safe to believe that the man dressed in black is ALSO taking over Christian Sheppard's body? We obviously now know that the island does not bring people back from the dead, so we know that Christian Sheppard is not actually alive. I believe that this guy is taking over different bodies in time in order to somehow find is loop hole. The question is why has he found is loop hole in Locke, and not necessarily Christian Sheppard.