Here goes nothing.
I think the end game of Lost doesn't involve Jack or Locke. Neither do Sayid and Sawyer factor into it. (Well they do, but not in the way we all think.) I think the story of Lost is not the story of good and evil or Adam and Eve. It's the story of Cain and Abel.
Wait a minute, Bodie. What?
First a recap. In "Lighthouse", we were introduced to a mysterious Wallace character. The 108 degree name was a name we've never heard before. However, I think we all know who Wallace is. It's Shannon Rutherford.
Yes, the leggy blonde is gonna play a big role in season six.
In "LA X", Boone, Shannon's brother, tells Locke that he was in Sydney to bring back his sister, but he saw that she was happy in Australia so he left her there. If I remember correctly, Shannon was in Australia with a guy. Maybe that guy is Wallace. Maybe that guy is Shannon's husband. Maybe Shannon Rutherford is now Shannon Wallace.
The fact that Hurley found Shannon's inhaler is no coincidence. Hardly nothing on Lost ever is.
How does that factor in to what we already know? Well we know that Sayid is infected with something, or someone, and we suspect that someone is Jacob. I think that its not a coincidence that it's Sayid that Jacob has infected, given the Iraqi soldier's fondness for Shannon. (They did have a thing before Shannon died, before Sayid went cuckoo on everyone for like 3 episodes.) Therefore, I think Sayid is a conduit for Shannon. He's gonna be the Cain in this story.
Abel, of course, is Boone. We all know who Boone's confidant on the island is. It's Locke. He even says that in "LA X" - If we crash, I'm sticking with you is not a callback. We also know that Boone and Shannon don't exactly see eye to eye, so what if their fight is one of epic proportions? Damon and Carlton have filled the series with biblical stories, so why not have the end game play out as a retelling of the story of Cain and Abel?
Here's my theory on the end game.
As always, I could be wrong on this.