My conclusion is that the "Flashsideways" are in a separate reality, as opposed to an alternate one (like bethsbooks mentioned earlier in the thread). Juliet said "It didn't work" to Sawyer, but dead Juliet said (to Miles) "It worked." I think both are true.
I'm guessing the point of this is to experiment with questions related to destiny/fate: perhaps their destiny plays out in different ways (on island v. in LA), where a few major events still happen (i.e. maybe Locke will be healed; maybe Charlie is 'supposed to die,' as Desmond insisted in season 3), and ultimately, they'll all end up in the same place no matter what form of reality leads them there.
Also, like SXBrase mentioned, I agree that they're showing the unintended consequences of blowing up the bomb. Things have definitely changed (though subtly - Rose's calm demeanor instead of her freaked-outtedness from Season 1); it seems the world changed way before the flight ever happened (as opposed to what they assumed - that the changes started with them not crashing, and that the crash was the only thing that would change).
However: I'm wondering if your Theory #1 might have some weight to it. I don't know if it's necessarily the end of the show but I'm unconvinced that this Oceanic flight is taking place in 2004. The reason I say this is because if you look at the underwater version of the Dharmaville barracks, they look totally demolished and in ruins like they did after that huge conflict with the freighter people (Keamy, in Season 4). Before the freighter people came, it was in pretty good condition; after, and when we see it in 2007, it looks pretty banged up. That conflict took place after (and because) the flight crashed. How can they be flying over it, in disrepair (sunken or not) if a) that timeline is completely separate, and b) those events happened post-original-Flight-815 (i.e. in September 2004 they cannot be flying over barracks that got ruined in December of 2004, sunk to the bottom of the ocean somehow, and had time to grow sea-plants and all that)? My head is spinning, so sorry if this is unclear.
Basically, I think the timelines will intersect at some point, and I think the flight we saw in the premiere may happen at a later date than the original one did.
I'm also questioning who is good - unconvinced that Jacob is a good guy. I have lots of thoughts on the temple and the murky water and Sayid, but I've already written a novel here. (Sorry.) Also wondering, how did Fake Locke know Real Locke's dying thoughts? Has he been in his head for a long, long time? Or, is he able to know the thoughts of the bodies he uses as his disguises?
I love this show.