*SPOILERS*
I agree with a large part of what Mana just said. The biggest problem for me is that Season 6 basically invalidated all the prior seasons with its metaphysical crap.
The writers could have come up with a very cool, time travel sci-fi ending of the show and instead they went for religion - nonsensical, dumb-looking religion at that. The glowing cave was dumb, Jacob and Smokey's mom was dumb, the cork was dumb, Jack becoming the new Jacob and having no clue what he was supposed to do was mindbogglingly dumb.
Why not simply have an alternate timeline created as a result of the Incident? Why not show us what the world would look like if Smokey actually escaped the Island? Why not have Season 6 be an epic struggle for the characters to restore the original timeline even if it means a good number of them who are alive in the alternate universe will die again if the original is restored? That seems like a pretty cool concept to me and one that involves a choice and a sacrifice at the end (Fate vs. Free Will, y'know). <_<
Oh, and after all the build-up, the "Adam and Eve" reveal was about as awful as anything the show put forth.
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There is always another rainbow...