This may have already been discussed to death, but I just finally got around to watching the episode last night. Great stuff, but it confused me on a couple points, annoyed me on another...but there might be a reason.
First, my confusion. Let me see if you saw what I saw: When Desmond gets blasted by a strong magnetic field, his 'essence' (soul, mind energy, whatever) is able to connect between the two realities. He can't be conscious in both at the same time, hence the passing out on the island. Right? But at what moment was he in the other body, aware of the other timeline? We didn't actually see any of that in the sideways flash, right? The reason I'm saying that is because when it happened before, he was really there, mentally. What they were showing us in the sideways reality didn't show him actually aware like that - it showed him getting flashes, just like Charlie or Jack or Faraday, but not completely aware. So does that mean they were really screwing with us, and the sideways reality was NOT what Desmond was actually experiencing while he was passed out on the island, but rather simply his sideways flash story?
If you follow that train of thought, it implies that the moment that the blast occured was actually when he passed out after touching Penny - he passed out in both realities. And when he came to, he had swapped places. The Desmond now on the island is the sideways reality version, and the Des with Penny is Island Des. Does that seem right?
It makes sense with his weird change of attitude and personality, especially on the island, and his odd look at both Widmore and Sayid. But that also means that while it looked like he was going to help Widmore, that was just because he ALWAYS helps Widmore - for sideways Des, that's an automatic response. Hmmmm...I really like that part.
Now my annoyance, that might still eventually make sense. This is the second time Des has gotten zapped by EMP. The first time, he also traveled, but we assumed it was in time. Now it seems like that was wrong - he traveled to a different timeline, not back in his own. At least I hope so, otherwise I'm going to be very annoyed. If the EMP sent him to another timeline this time, it better have done the same thing before, otherwise it's just a writer's crutch. And if it did send him to another timeline before, that says there are many - which makes it a bit more confusing as to why they have to worry about this particular one so much, or why it's causing specific problems.
Oh, and my last annoyance that I doubt they'll do anything to correct - they are acting like it's only the people involved with the island that are mucked up with two sets of memories. But every human being would have two sets of memories - they've all lived (or died) through a section of the two timelines. I've always thought this was one of the weaknesses of King's use of the same theme in the second book of the Dark Tower.