I have seen a lot of people speculate that the alt scenes last night were in fact the final scenes of the series. The general consensus seems to be that Jack remembers everything because he is acting disoriented. I don't think this can be the case. First, if Jack remembered everything, he did a real good job pretending not to know anyone, including his beloved Kate. He is also very upset to have lost his father's body, even though he is not around anyone he would have to "act" around (prior to his scene with Locke). It is weird that Desmond is on the plane, and it is weird Jack has a cut, but it's been one episode.
Then the island is underwater. If we are supposed to believe Jughead went off and changed everything, then are we also supposed to believe that it is the reason the island is underwater? And if that is the case, how are the Losties on the 2007 island not underwater? Never mind the fact that the island looks pretty good for being nuked and underwater. If the island is underwater because of a battle we have yet to see, we have to remember that the island is supposed to be in 2007 (or, at the very least post- plane crash because the remnants of their camp were there) so in order for that to change anything pre-2007, there would arguably have to be more time travel pre-battle, and we've been told they are done with that.
Another thing - if the alt scenes are the end as a result of something we see happen on-island, how are they going to resolve all the character dramas? The producers said everything will be resolved and so far in alt-land, it looks like they are creating new conflicts and story lines- Kate is already on the run again, Hurley is a successful businessman, and we still have more to learn about the other characters (Claire's life is already clearly different).
I have seen it proposed that alt will be the original time line as it played out without Jacob and I am convinced this is the case after the premiere. Jacob has "brought" people to the island. He brought black rock, I will venture a guess he had something to do with Dharma coming, and MIB appears to be someone "brought" to the island as well, but who is at odds with Jacob's plan (which is why he wants to go home). What Jacob's plan is, I am not sure. I think it's obvious now that he brought the plane and more specifically, the key Lostie characters. His list of names inside the guitar case and his non-surprise at being murdered indicates that this is a very well thought out and orchestrated plan on his part. If this is all true, the big question ultimately is...why? Why these people? Well to answer that we would have to see what these people did for Jacob to decide to seek them out and "alt" would be a way to do this. This would be consistent with the assertion tha! t flash backs and flash forwards aren't being used this season - we are merely just being shown another version of the story. It would make it easier to give the audience closure for the characters because they wouldn't have to worry about wrapping up these new plots that are unfolding in the alt-line - instead, we may just see all their worlds collide to result in whatever it is that attracted Jacob to them in the first place. And as for Juliet's statement after she died, if she can flash to her alt-life before dying, then you can just as easily argue that she is flashing to her life pre-Jacob. Plus that statement is pretty vague and the fact that we all seem to think she is flashed to some other version of her life probably means we're wrong!
And finally, MIB pointed out that they all had pathetic lives and Locke was special because he was the only one able to recognize that and appreciate how the island could change that. Their lives still look pretty pathetic so far (definitely Kate, Sun, and Jin - and Locke is still in a wheelchair lying about his trip). Are we supposed to believe the big ending is that...they go back to their pathetic lives and live pathetically ever after?