Okay, many of my theories have revolved around my belief that the John Locke that is with Ben when he murders Jacob is in fact the "real" John Locke and not some body snatcher (MIB). I have explained why to some degree, but this theory is basically a bunch of reasons why I think Locke can't be anybody besides Locke, and I'll end it with my overall theory.
First of all, when Locke is first discovered by Cesar and Ilana after 316 crashes, he seems rather confused and dazed. He acts like he really just woke up from being knocked out or something. He claims to not know how he got there and tells Cesar when he sees Ben that "That's the man who killed me" and that "the last thing I remember is dying". WHY would MIB say these things to Cesar??? He could just lie to him and Cesar would have been much ls suspicious of him and wouldn't have attempted to kill him (When Ben stole the shot gun and shot him).
Secondly, MIB obviously KNEW that Jacob lived in the statue and after MIB told Jacob that he was going to find a loophole, Jacob said "When you do I'll be right here", so WHY would MIB as LOCKE need to ask anyone where Jacob lived? He wouldn't have to ask Richard or anyone else where Jacob was, he could just go there with Ben and kill him.
Thirdly, Locke seems to genuinely want to help Sun get back to Jin, and goes out of his way to comfort her and be nice to her. Why would MIB do that? Why would he care about Sun at all??? He wouldn't most likely... And when Locke tells Ben in "Follow The Leader" that he's not concerned with re-uniting with his people, and Ben responds with "But you told Sun that you would" and Locke says "I know that's what I said, BUT that's not why we're going to see jacob" SO maybe he is the real Locke and he is still planning to re-uinte with Jack, Jin, Sawyer, Hugo, etc. after he kills Jacob with Ben. He didn't deny the fact that he told Sun he'd help her find Jin, which is something MIB wouldn't want to do or care about even speaking about.
Fourth, 316 lands on he HYDRA ISLAND, and there is quite a bit of doubt that the monster can travel to the Hydra Island. The reason I say this is because most believe Locke to be either MIB or the smoke monster, and most people believe that MIB and Smokie are one and the same. When Sun and Frank go back to the main Island, while Ben, Locke, Cesar, Ilana, Bram and the rest of the survivors are still on the Hydra Island, you can distinctly hear the smoke monster as Frank and Sun arrive at the docks on the main Island, and Sun tells Frank that it's probably just an animal when she knows what it is. How can the smoke monster/MIB be on the main island if Locke is clearly on the Hydra Island with the other 316 survivors??? He can't be. This is assuming that MIB is the smoke monster, or at least an argument against the fact that Locke and the smoke monster are one and the same, because with the above info, they can clearly not be one and the same, physically impossible.
Fifthly, Locke has all of his old memories of before he died, and acts very humanly for the most part... he tells Ben that he is only hoping for an apology when Ben attempts to rationalize why he killed John. Why would MIB/Smokie care about an apology. Why would he make small talk with people and be kind to Sun, Frank, etc... ?
Sixth, I think that the reason Locke knows so much more about everything is evidenced when in "Dead is Dead" when Ben says that "it doesn't work like that, I can only summon the monster, I don't know where it actually is" and Locke says "I do" and leads Ben to the smoker monster, and when Ben asks him how he knows where he is going, and Locke says that "he just does", and Ben then gets upset and says "Well how does that work exactly, the knowing, did it come upon you gradually or did you just wake up one morning knowing all the answers?" and Locke tells Ben that now he knows what it was like to be Locke. Locke seems to know all about the temple, and I believe this is because he has been there and this is why he knows so much stuff now.
So my overall theory with Locke is that when he was pushed out of the window by Anthony Cooper, he actually died before being somehow brought back to life by Jacob. HOWEVER, Jacob brings Locke back to life in a DIFFERENT REALITY. In the season two finale, Desmond turns the fail safe key and implodes the hatch with Eko, Locke and himself still inside. When the key is turned, the bubble surrounding the island lights up and buzzes really loud. I think that when the fail-safe is turned, it "finishes off" what the Incident had started - all of the Island's electromagnetivity is released, and the Island stops "moving" in space. The button being pressed every 108 minutes after the incident allowed the Island to continue being moved in space, but not time. It still moved in regular time for almost 30 years while moving in space so that it could never be found - until Desmond turned the key and the island lost it's energy and stopped moving completely in space and time. When Ben went! to the Orchid and turned the donkey wheel, he finally moved the island in TIME, and when it moved back and was skipping, whatever happened always happened, but just not in a linear fashion. When Locke turned the wheel and the island ended up in 1977, I think everyone who went back in time went back to that same reality and created the events leading up to what they had "already" been through.
Meanwhile, the Island that 316 crashes on is in a second reality that was created when the fail-safe key was turned. The Island was released of all it's energy and when Locke woke up, his neck looks all red and marked up, and he can't speak and looks and sounds like he had just been strangled. I believe that this is because when Locke wakes up in the beginning of the third season, he is waking up in a second reality that was created when Desmond turns the fail safe key, which is why he wakes up in 1996 - in a separate reality in which Eloise must get him "course corrected" so that he ends up back on the island. Instead of course correcting, I think that when the hatch implodes, Locke is somehow transported to the Temple and is met by someone who wants Jacob killed, and they tell Locke how to do it and Locke agrees, and waits in the Temple for 3 years until Ajira 316 crashes and he goes to the Hydra Island to begin his process of murdering Jacob via Ben. I think that when Loc! ke wakes up in the beginning of season 3, he is actually waking up right after Ben kills him in the other reality. I think when Locke is pushed out of the window he dies and when Jacob revives him, these are directly following the events of the hatch imploding, because Locke mind-skips back in time right to his death, and Jacob gives him a second chance to "course correct" so that he will end up back on the island, just like in Desmond's case. This is why after he is in the wheelchair, Abaddon continue to try to alter his life so that he "gets to where he needs to be". I think the difference is that like Desmond, he can remember vaguely the other reality. I think this allows Locke to get back on his "path" and end up crashing on the island via 815 the second time around, and this is when he gets his "second chance" because when he wakes up in "Further Instructions" he is waking up in the second reality in his body that was brought back to the island on 316 when Ben kills hi! m, so he has all of his memories from the previous reality, ex! plaining why he tries to kill Naomi and such, and why he seemingly knows why and when certain things are going to happen. Basically, I think Locke is killed by Ben so he can be revived by Jacob in the second reality with his memory of the first one in tact so that he can fullfill his destiny, which we have yet to know what it is.
I know this sounds confusing, and it is, but I think when Ben kills Locke, Locke wakes up right as he dies in an alternate reality, in which the hatch has seemingly just exploded. Locke apparently keeps dying in one reality after another but continues to "know whats going on" because of Ben and Jacob's interferences. I believe that the Locke on the beach in "Bentham" is the real Locke, but one who knows things that none of the other characters do, because they haven't yet died and woken up in the next reality, or something along those lines. I believe that we will see Jack, Kate, Sawyer, and many other characters die, only to wake up in a surprising different time or reality, perhaps before or after some of the events that have already happened happened. Maybe Jack and co. will die in the beginning of season 6 and end up waking up in the next reality, created after the hatch explodes via Desmond, and they are captured and brought to the temple and brought up to speed by some! one as to what exactly is going on.
I think that season 6 will be about us seeing the main characters dying and waking up in another reality, only to end up on the same "path" that was always "meant to be". I think Jacob has something to do with this, obviously, and probably Ben too. All the "who is good and who is bad" stuff is too much of a headache for me, and to be honest trying to explain the time traveling and alternate reality stuff is nearly impossible to do, but these are my basic thoughts on why I believe that Locke is Locke and that he will end up being the hero in season 6.