My theory about The Man in Black being William, to elaborate, is that we are seeing someone play the game for the first time as a young man, and then for the last time as an old man.
William arrives for the first time, the train, the sets, the woman who introduces him to the game, and his hat are white. I'm also wondering if he isn't involved in the incident Bernard mentions.
His final time in the game, the time he intends to maybe die in the game, or maybe to become part of the game forever as a clone or something, he's playing it as a "straight evil" character. Though I suspect he's played the game both ways many times in 30 years.
I was buying into the theory of different timelines as well, but I feel that episode three threw a bit of a wrench into that idea.
Again, like I said earlier, the show is doing a good job of "hiding" it's timelines, so any evidence can be easily dispelled by future storytelling...however...this is the reason it threw a wrench into the two timeline idea to me...
We see Bernard talking to Dolores after we've already heard them discussing that the hosts are talking to someone named Arnold. So we are led to believe that this would be in the "now" timeframe. They've made it a point to mention that the hosts are hearing disembodied voices.
We then have Dolores end up killing the guy in the barn...after she hears a disembodied voice. I believe this means that it's also in the "now" timeline.
After she rides away from the farm, she ends up running into William and Logan. So, she has run into William and Logan in the same timeline that we are learning that the hosts are hearing the voice of Arnold, which would seem to be the "now" timeline.
When the Man in Black was going on his search for the entrance to the maze, a couple of techs discussed him. The setting that they were in looked no different than the setting that we see in the "now" timeline, so that leads me to believe that the Man in Black is in the current timeline, and since we have seen Dolores run into William and Logan in the "now" timeline that says to me that there aren't two different timelines.
Now, again, the storytelling hasn't been very transparent with it's showing of time...so it's entirely possible that the scene when Dolores runs into William and Logan is ACTUALLY something completely separate from the "now" timeline...for instance, in the next episode we may see William and Logan accompany her back to the farm and come across Teddy's body, which would clearly indicate that Teddy was there which would of course tell us that her running into them was from a different playing of the story than the one where she kills the other dude.
