Dualism permeates LOST to its core.
Each season is constructed around a binary explored through the characters and their interactions:
Along with those binaries, each season of LOST asks a fundamental question.
"How will we stay alive?"
"Having learned how to survive, in what should we place our trust?"
"What motivates us?"
"How did we get where we are?"
"Do I control my own destiny?"
In the question of Fate vs. Free Will, Season Five's organizing principle was Daniel Faraday's maxim: "Whatever happened, happened." Try as they might, the time travelers could not change their destiny. Sayid's decision to shoot a defenseless 12-year-old boy affected who Sayid is, but it would not result in a Ben-less future. Similarly, Ben and Sun were left in 2007, impotent to affect their goals, reduced to blindly following John Locke.
But somewhere along the way, that organizing principle (as well as Faraday's own attitude) changed. Though Faraday would lose his own life to "whatever happened"
Jack was emboldened to find a "something big enough" to alter history's (and his story's) course.
So, with the explosion of an atomic bomb (Jack has never been one for subtlety), we're left in the same boat as Ms. Hawking: for the first time in a long time, we don't know what's next. In that way, Season Five's finale most resembles the mind-freak of Season Three.
"Through the Looking Glass" was so unsettling precisely because it was the first time that we (the audience) couldn't know what was to be next. Until that point in the show, we were assured that no matter how bad things appeared in the flashbacks, eventually our lostaways would be on the island, walking...
But all that would be set aside when it became manifest destiny that our Losties would escape the island.
Unfortunately, that's where "The Incident" fails to resemble the Season Three closer. We're left with no clue of what's to come next. All we can speculate upon is the paradox created should answer yes to this simple question:
"What if it worked?"
If Jack really did succeed in disrupting the events that lead to the crash of Oceanic Flight 815, then the plane landed in LAX from Sydney as planned on September 22, 2004. However, if the plane landed in LAX, how would Jack have traveled back to 1977 to set off the atomic bomb? Mustn't it be simultaneously true that Flight 815 crashed on the Island and that it did not? This is LOST's Schrodinger's cat, on a much grander, mythological scale.
Certainly, Damon Lindelof and Carlton Cuse built in smaller scale conundrums. John Locke's compass...
is an artifact without provenance. Richard Alpert's investigations into the young John Locke...
function precisely the same way. Richard never would have looked into the young John Locke, had Locke not told him to. But Locke never could have told him to had Richard not looked into him first.
Such puzzles are only the beginning. LOST's final season has its work cut out. But, to the many questions we might ask:
The smoke monster
The island itself
We can go on these few things: The writers have pointed out on numerous occasions that their interests reside in the characters. The mythology of the show is just a method of exploring those characters. So, we can expect to continue to learn about Jack, Kate, Sawyer, Hurley, and the rest. Perhaps we will even get the opportunity to re-acquaint ourselves with some old friends...
And some friends reborn...
What will be Season Six's question? I'm sure we will revisit Faith vs. Reason.
I'm sure we'll see more about Fate vs. Free Will
Perhaps Season Six will really be about Jacob vs. The Man in Black
But I know in just a few hours, we will know the answer to at least one question.
"What if it worked?"
 In this way, the early part of LOST's fifth season followed the Harry Potter school of time travel.
In Prisoner of Azkaban, Hermione is given a locket with the ability to turn back or "rewind" time. Its initial purpose is to allow Hermione the extra time necessary to complete her over-loaded course schedule. But, as Dumbledore intimates to Harry and Hermione, it can be used for other reasons. What's interesting about the conclusion of the story is that, as Harry and Hermione travel back in time and help their past selves out, they don't "change" what has already happened. They merely become aware, through their more knowledgeable perspective, of events that were not at first what they appeared. This was most explicit in Harry's bittersweet discovery that it was not his father who sent the Patronus that saved both he and Sirius, but he himself.
 This was part of the beauty, at least initially, of the producers' decision to follow the Harry Potter school. Not only was Sayid powerless to prevent Ben from becoming Ben, but any action he did take would only end up being a part of why Ben was the way he was. Even the choice not to act (i.e., Jack's) would prove full of consequence. This was one way I thought the producers' actually dropped the ball when they pulled the whole "if I save Ben, he won't remember any of this" card. I WANTED Ben to remember. I wanted his attitude toward Sayid, which engendered Sayid's attitude toward him, to be dependent on Sayid's choice to shoot Ben as a boy. Alas, they decided not to take it quite that far.
 This might be called the "Back to the Future" school of time travel.
Marty McFly can travel forward and backward in time, seeing to it that the universe changes in (to him) necessary ways, even as he does not.
What's on my mind?
Dualism permeates LOST to its core.