So here's something I've been a little confused about:
My understanding of the parallel universe is that it's the universe in which the bomb was detonated and therefore stopped the incident from happening (so that the hatch is never built, Desmond never leaves the hatch unattended, and plane never crashes). If this is the case, that doesn't erase the fact that the people who detonated the bomb in the '70s are still the characters we know, but not the same versions who land safely in present day. Sayid did shoot Ben and he was brought to the others.
That's the inconsistency I'm seeing. Because if Ben was brought to the others for healing, then he wouldn't have escaped the island with his Dad when the bomb was detonated and, if somehow he managed to get off the island, he probably wouldn't be as amicable with his father as he was in this episode.
Now, if in fact the reason that the island is underwater is from something entirely different from the atomic bomb being detonated, then all of this is fine, but the only reason for it to be detonated is because the 815 survivors came back and detonated it.
The current timeline, is what would happen if Mile's theory was correct (the bomb cause's the crash), and the alternative timeline is if Faraday's theory was correct (bomb screws up island). I think thats pretty significate, and I swear Miles is becoming more significant character, he is awesome.
*spoilers from episode 8 below*
I think the "bizzarro world" that we're seeing is a world without Jacob. Remember how he stepped in to everyone's lives and "touched" them somehow, at a crucial moment? And keep in mind that the island is underwater. It's as though all of the "islandy" stuff never happened to anyone. And notice that some people were affected more than others. Some characters have had only a small detail of their lives reversed (like hurley having good luck), while other people have their entire character inverted (like sawyer being a cop).
That's just one possible idea, though. I really haven't thought about it hard enough to see all the possible consequences of a "world without Jacob," and I'm sure there's more to it than just that.