I was so excited to see that some people did not dismiss my "Future theory" outright.
I can picture this: The ship that we all thought was the Black Rock comes ashore, and the Losties disembark. Huh? That's right, the ship comes in at some point in the future - only we will not be explicitly told this - which is why it's so confusing. So, while we've been "away", there has been over a year of off-island real-time to account for 2008-2009(and a little bit more on-Island time). I think that is the reason for the logo color change at the end of Season 5 - from white on black, to black on white. I think it may have been meant to symbolize the fact that we just crossed the time divide. So while the show used to be flashing back (to dates in the audience's real-time past, we will now see what happens in the future...will it be WWH or will it be changed? And I think, the last episode will end in real-time - on May (fill in the air date), 2010.
OK - this part is a longshot, but perhaps the Incident was so catastrophic that the world was indeed "destroyed" and had to be built from scratch. That would explain all of the early civilization-revisted references. And, if you take a look a the transcript from Jacob/Nemesis' scene in the Incident, the language is far too modern/casual to be speaking in the 1800's. At least that's my thought. Think Planet of the Apes (for those of you old enough to remember :) - the whole time you think the apes are in the past - until the last scene, when they show you the Statue of Liberty destroyed - and you know it's the future.