Ok this may seem really far fetched, and i know this probably isn't true, but you got to keep in mind, that probably and the right explanation usually don't match on this show.
And what i've got from this episode is that MIB may be in fact the real John Locke.
Well maybe not the real body of course, that one is buried, but i'm not talking about chaneling some thoughts he once had. So here's my thoughts:
1st - MIB asks Desmond who is he. He answers "well of course.. You're John Locke". Notice the face on MIB, he doesn't nod, he doesn't seem he successfully disgised himself, he looks stunned! Why would he seem stunned? He's portraying John Locke after all.
2nd - Desmond tries to KILL Alt John Locke. Why would he do that? Because he saw him who he thinks it's Locke on the island through the well and now he is taking revenge on the ALT because he thinks Locke is bad?. Sure this is probably true. Just one thing - Desmond is supposed to be enlightened since last episode. And i'm sorry i don't really believe he is enlightened that he didn't know there was something fishy about "that" john locke.
3rd - His using of the knife to build that spear, his "don't tell me what i can't do", his crazy mother (remember the real john locke's mother?).
4rd - This is Lost. And John Locke has always been one, if not the most iconic character of the show. And was he really killed at the end of 4th season to be replace by MIB only that the show wouldn't lose Terry O'Quinn?
5th - MIB said what Locke was thinking when he died. Locke died OFF the island, MIB is stuck IN the island. How would he know that?
Again, yeah probably. But probably and Lost do really match?
If MIB and Locke aren't the same or at least very connected (much more than simply channeling some thoughts) then Desmond was REALLY dumb in this episode, and i do not think this is the case at all.