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So, I am finally ready to hazard a guess at what the significance of the alt timeline is, and some of the bigger themes of the show/this final season...
Seems to me, LOST is ultimately about the concept of Destiny vs Free Will.
Now it seems to me that by the end of the show one of these two concepts will have beaten the other and will be proven over the other. That is to say, either Destiny is absolute, or freewill exists and is very powerful.
But choosing one over the other, well, I don't know if I like that.
So, my guess is that they both are the case. And not just as a system of checks and balances,
I believe that the original timeline is the pro-destiny timeline, and the alt is the pro-freewill.
This leads to the writers being able to end the show by never actually choosing one over the other, but at the same time doing just that.
Destiny(Orig): The candidates were on the 815 because it was their destiny.
Freewill(Alt): Random people with connections were coincidentally on a plane together
Think about it, the only reason the alt exists (as far as we know, but that remains to be seen) is a result of Juliet's freewill in destroying the island. Jack and Locke meet in lost luggage- but Helen uses freewill shredding the card and saying no to destiny.
Claire goes into labor, but uses freewill and decides to have her baby later.
What I'm trying to say, quite plainly, is this:
Original Timeline= Destiny
Alternate Timeline= Freewill