I'm guessing that we're seeing two different timelines.
In the one we see that the Island has sunkunder the ocean, that the main players made it to LAX with some exceptions (Christian) Boones sister etc and that some key items, the body, Locke's knives have vanished. I'm assuming that when Juliet hit the bomb it exploded and combined with the energy pocket to split realities.
In the second, the bomb failed to destroy the energy pocket so events didn't change and they are still on the Island. With Sayid's death, I'm almost convinced that Jacob has found a loop hole of his own and he's either all the way in or partially in Sayid. While its clear that Smoggy wants to leave the Island and go home, Jacob is there to keep him on the Island. In effect I think that the Island is suppossed to be like a prison to hold ultimate good and ultimate evil occupied and contained. I also go back to the religious symbols like the Anhk (sp?) and some of the gliefs on the walls and the large statue that are very egyptian in their content and wonder if these two represent Ra the sun god (Jacob) and Osirus god of the dead who has a stunning similarity to the statue.
I have a feeling that the two realities also at some point have to merge, perhaps if Jacob is able to defeate Smoggy he will grant freedom in gratitude, because I think its clear that their lives in the non Island reality might be easier, they are not good lives.
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My name is Ozymandias, King of Kings;
Look on my Works, ye Mighty, and despair!
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