Many people have attempted to make sense of the Lost Finale, one of the most anticipated television series finales in recent memory (Only the Sopranos comes close in my mind). I have read many recaps and responses to the finale and will make no attempt at a systematic or even full discussion of the finale here. Instead, I would point you to my favorite response, which of course, is that of my wife and her inclusion of Travis Prinzi's response which I loved.
What I would like to do is clear up some misconceptions about the finale (at least from my point of view) and to point out a couple of interesting elements of the episode that I have not seen discussed elsewhere.
Misconception 1: the nature of the flash sideways reality (there are actually several misconceptions here).
Many people are confused by the flash sideways. This is understandable considering that the producers and all of the commentary this season led viewers to believe that the flash sideways was an alternate reality, one made possible by the detonation of the nuclear bomb in the last episode of season five, "The Incident."
In a supreme twist, the flash sideways is anything but an alternate reality, one that exists instead of the reality we have been watching for five seasons. No, the flash sideways is what another blogger has referred to as a "flash upwards." I like that terminology and will thus borrow it from here on out. What the flash upwards refers to is Lost's version of the afterlife. That is the most simple way to put it. This leads to misconception 1-A: when does this reality occur? This reality does not occur beside the given reality, it is outside of it. I would say "after it," but that is not really correct. There is no time in the flash upwards. It is not related in time at all to the shows earthly reality. Many people seem to want to relate the time in the flash upwards to the timeline of the show, and this simply doesn't work or have any meaning. This concept of a timeless reality seems to be one of the hardest things for some people to grasp. For a discussion of how this might work, intellectually, see Augustine's discussion of God and time in his Confessions Book 10.xii ff. Misconception number 1-B about the flash sideways reality is that it is purgatory. While this is not entirely wrong, it is mostly wrong. Purgatory is a place for the purging of sins and for becoming holy enough to enter paradise. There is no purging of sins in the flash upwards. It is not about becoming "worthy" or "holy" enough to move on. Rather, it is about remembering and letting go. If anything, the purgation of of sins happened to all of our beloved characters on the Island and in their earthly lives. No, the flash upwards is not purgatory, it is about remembrance and letting go. The only relation to purgatory is that both occur in the afterlife. Misconception 1-C about the flash upwards is that is it "not real" or is in some way imaginary. Christian, if we are to believe his words to Jack in the church, clearly refutes this view. He claims that he and Jack and everyone in the church is real. This is not some imaginary dream. It is as real as the lives all of the characters lived. This is just the very real step after death for all of these characters. Misconception 1-D, and I use the term misconception lightly here, for the show does not give us enough evidence to be clear here, is that the flash upwards reality is a "creation" of the Losties. Christian does say that "this is the place you all made together so that you could find one another." Many people have made a really big deal about this, claiming that the flash upwards only exists for the people in the church, because they "made" it. In my opinion, this is a misconception. I believe, with no rock solid evidence, that the flash upwards reality in general is the afterlife of all people. What the Losties "made" was their memories of each other and the ability to find one another and move on together after life. For a helpful analogy to the flash upwards, see C.S. Lewis' The Great Divorce, which, I believe, paints a similar picture of the afterlife.
Misconception #2: One could only awaken and remember when confronted with one's soulmate. A nice idea, but one that becomes absurd when followed through. This misconception has led many to mock and even be angry at Sayid's awakening in the arms of Shannon. Surely Nadia was Sayid's soulmate, right? Of course, but if we take the soulmate view, then Jack's soulmate was partially Locke (he had a brief flash of memory with him), partially Kate (he had a little longer flash with her), but ultimately, Jack's soulmate was his father's coffin. Any fetishes for that? Also, Kate's soulmate is Claire giving birth, and Ben's soulmate is Desmond beating the crap out of him. Really, a better explanation is that moments of intense emotion and enlightenment on the Island are responsible for the awakening, not necessarily one's soulmate.
Finally, I will note a few peculiarities that I have not heard discussed, but I think shed light on the flash upwards reality.
First, time in the flash upwards reality is not linear in the same way as the earthly reality. Consider that Locke and Sun end up in the ER at the same moment, but this does not appear to be possible given a rigid timeline. Sun's timeline goes like this. She and Jin land at the airport, check into the hotel, the next morning they are confronted by Keemy and taken to the restaurant where Sun is shot. So, Sun would arrive at the ER the day after flight 815 landed.
Locke on the other hand lands at the airport, reports back to work, presumably the next day when Sun is shot, is fired, visits Rose at the temp agency, is assigned a job as a substitute teacher, gets to know Ben and plays along with Ben's attempt to seize the principal position at the school, only finally being run over (or under) by Desmond. Yet, he arrives a the ER at the exact same moment as Sun. Interesting, time in the flash upwards is a little bit bendy.
Second, when Ben and Locke have their conversation outside of the church, Ben has totally changed. At the beginning of the finale, we see a shot of Ben who is still beat up from his encounter with Desmond. His hair is short, and I believe (not having a DVR) that he is still in a sling. When we see him outside of the church, he is fully healed and has longer hair. So, physical reality in the flash upwards is also a little bit bendy. Locke is also different in that conversation. Clearly, he is able to walk, but he also bears no remnants of the physical trauma caused by the accident, which he still had in his awakening conversation with Jack. Finally, Kate arrives at the church in her black cocktail dress, but when we see her in the church, she also has changed. It appears that once people are awakened in the flash upwards, time and physical reality are pliable.
Thus, the flash sideways is truly real, but physical and time laws do not behave as they do in the earthly reality. Hope this adds to your understanding of the Lost mythology, or at least provides fodder for further conversation.