"Don't tell me what I can't do"
That line from this week's episode (The Substitute) struck me as odd. After all, we all assume Locke on the Island is the MIB now, not the Locke we learned to love in previous seasons. And yet, that is an exact line we heard "real" Locke use on numerous occasions throughout Lost. Why would fake Locke use that line?
My answer to that question is the Locke we have known in the previous seasons was always under the influence (perhaps sharing the same body?!?) of the MIB. Supporting facts beyond the line used this week include: young Locke's drawing of the smoke monster noticed by Richard and fake Locke reporting to Ben Locke's last thought while Ben was killing him. There are probably others. But it seems the "real" Locke was under the influence of the MIB for quite some time.
Continuing this thought, it seems Locke in the alternative timeline is much more relaxed and aware of his limitations. I cannot envision "alternative timeline" Locke using the line above. Therefore, I guess/speculate that alternative timeline Locke is not under the influence of the MIB.
Perhaps the alternative timeline is a timeline in which the Losties are not influenced by either Jacob or the MIB. And the timeline we have known up until now is a timeline in which the Losties have been influenced by both Jacob (as we have seen) and the MIB (not yet confirmed). That is, the timeline we know is a "fated" timeline (the Losties under the influence) and the alternative timeline is a "free will" timeline. We know fate vs. free will is a big theme of the show.
But that is a much bigger theory.....