Even before the episode began, it was clear that the final chapters of the novel that is "Lost" would leave some fans displeased and unfulfilled. Nothing that happened in the finale was going to change that fact. Instead of trying to please everyone, Damon and Carlton did what they felt was best for their own story, starting right from the beginning of the sixth season.
"Lost" was originally conceived as a story about a group of plane crash survivors with a variety of personal issues who find themselves facing mysterious and dangerous circumstances. And sure enough, that's what the first season was all about: characters searching for or resisting redemption, with the mysterious properties of the island facilitating that process.
As the series comes to a close, it is abundantly clear that the series remained true to its original premise. While the writers definitely fed the hunger for answers to the innumerable questions regarding the nature of the island, it was never about searching for the truth about the island. It was about the characters and their journey to personal enlightenment.
The writers repeatedly made the observation that the story was being told from the perspective of the characters. And as such, the characters would have to be the ones to raise the questions and demand answers. One could quibble over whether or not the characters would fail to ask about certain details or press for more definitive answers, but these were also characters under extreme stress, internal and external. More often than not, the gaps in information were consistent with the notion that the character themselves would not know to ask for those answers.
For example, the "rules" for Jacob and his brother (here called Adam; otherwise known as the Man in Black) were never explicitly explained. They were generally given a basis, and the audience had some context to understand the effect of the "rules", but the character themselves were only concerned with how the "rules" affected them. And that is how the "rules" were treated.
The treatment of the Source in this finale is no different. Generally speaking, some ancient people managed to create a device which channeled the geothermal energies under the island into an intense electromagnetic/temporal anomaly, including the ever-important water from the island as a coolant. The device that created/maintained the Source was the metaphorical "cork" that held back the darkness that could destroy the world. There is no reason to think this simple chamber was the full extent of the device.
In more definitive terms, it's fairly clear from this episode that removing the "cork" would sink the island. But it might also unleash the geothermal energy, perhaps in the form of a supervolcanic eruption. That would result in a worldwide darkness that would, if powerful enough, kill all life on Earth.
Now, one could quibble about how an island that can move through space and time could still be connected to a specific geothermal source. And of course it's hard to reconcile, rationally, how the Source would then imbue an individual with supernatural powers or, in essence, turn a human being into a non-corporeal being of black smoke. This is because those elements don't really need to be explained on that level for the purposes of the story.
If anything, the writers harken back to the mystery of the Swan Station, both visually and thematically. The Swan Station, according to the Dharma Initiative orientation film, was built to contain a dangerous pocket of electromagnetic energy that, if unleashed in an uncontrolled manner, would destroy the world. As the characters themselves note, nearly everything about the Source is metaphorically identical. Just as the Swan Station and its unusual properties were never fully explained, the Source is only treated insofar as it has meaning to the needs of the characters.
The resolution to the overall series arc is relatively simple. Whether or not Jack actually reasoned out the best way to resolve the conflict is a matter of debate. It certainly seems as though Jack was just feeling things out as he went. But in essence, the island was "healed" using the age-old notion of stopping the heart, temporarily killing the patient, and then starting the heart back up again.
While Jacob and Jack both derived power from the Source, it's fairly clear that Adam/MiB did so as well. The clue to the solution of Adam's power was revealed as soon as Richard began to age again. Once the connection to the Source is severed, mortality resumes. Once the Source was extinguished, Adam became mortal in the form of John Locke.
Thematically, it always had to come down to Jack and Locke in a fight to the death. Of course, in terms of the mythological cycle at the heart of the story, it also had to come down to Jacob (in the form of his Candidate, Jack) and his brother (in the form of his chosen, Locke) in one final struggle. Both conflicts were based in recognizable human struggles with free will, destiny, and redemption.
For this reason, it may have been thematically more pleasing if Jack had been able to overcome Adam/Locke once and for all. It's always more satisfying to see good conquer evil. But Jack was never explicitly good, and while Locke was never explicitly evil. (While Adam/MiB was certainly evil, that wasn't necessarily his innate nature, and there is plenty of reason to doubt that Jacob was definitely good.)
But one issue was always Kate's role in the story. Her role in Adam/Locke's demise gives her prominence in the story more meaning, as does her eventual decision to leave the island and help Claire raise Aaron. It also allows Jack to survive long enough to see the story through to the very end in the most symmetrical manner available. (Note that Jack's mortal wound is in the exact opposite site of his body from the wound he incurred in the crash during the pilot.)
With the Source extinguished and the island preparing to blow, Jack's impending death and Adam/Locke's death represent the end of the cycle that began with the birth of Jacob and Adam. The old rules no longer apply. If there is one moment that doesn't quite work in this finale, it's the transfer of power between Jack and Hurley. While it is necessary for the overall story, the specific details don't seem to unfold in the right order.
Leaving out the details of the power-transfer ritual (which may have been meaningless ritual in the first place), the Source didn't exist at that point. So it doesn't make sense for Hurley to be given the role of keeper of the Source until the ancient device is restarted. Of course, it was cleaner for the purpose of the story for Hurley and Jack to say their farewells before Jack went into the Source chamber, but it was a bit sloppy.
Similarly, in "Across the Sea", it seemed as though the Source would render a living human being incorporeal, trapping them in an endless existence, trapped between life and death. By the same logic, Jack should have been similarly affected once the Source was restored. If "Across the Sea" established anything, it's that the Source had no conscious will of its own; while the "rules" of the island were based on the individual demands of the Source's keeper, the Source itself should have been bound by its particular nature. But in the overall scheme of things, that's a minor annoyance that doesn't change the point of the plot.
Structurally, the purpose of the Ajira 316 flight and the manner that it arrives on Hydra Island in the fifth season is fully revealed, as is the overall role of Frank Lapidus. It's great to see Richard and Miles make it off the island, and as often noted in reviews for previous episodes, it was evident that Sawyer and Claire would leave, if they managed to survive the final showdown. And the survival of Rose, Bernard, and Vincent was a nice touch, reinforcing the idea that there would always be people on the island.
Had Jack survived, it would have made sense for Hurley to be the leader of the eventual New Others. With Hurley now acting as the keeper of the Source, Ben is a surprisingly perfect alternative. This is really the end of Ben's own redemptive arc, and brings his character evolution to a satisfying conclusion.
As Jack notes, the properties of the island that trapped people there were unique to Jacob. He wanted to limit access to the island and ensure that Adam/MiB never left. That was how he chose to protect the Source. Hurley can set the "rules" however he wants, which will inevitably give Desmond the ability to leave the island once and for all.
So in terms of the overall island story, from the beginning of the pilot to the moment that Jack dies, it all hangs together fairly well. There will inevitably be details that don't seem to add up on closer inspection (the depiction of the Others and the whole mess surrounding the cabin, for starters), but given the real-world factors at play in the development of the series, this is hardly unexpected.
Of course, that only covers one aspect of the finale, and particularly the season.
This episode reveals, once and for all, that the "Lost X" timeline was, in fact, not an alternate timeline. Ironically, the producers tried to say this from the beginning; they made it very clear it was not a competition. Those who speculated that the "Lost X" timeline was a kind of epilogue or denouement were right on the money.
Everything in "Lost X" takes place apart from the main story. Once twice does someone in "Lost Prime" interact with "Lost X": when Juliet is about to die in "LA X", and Desmond's unusual journey in "Happily Ever After". Juliet's reason for peering into the pseudo-limbo of "Lost X" is obvious; she was on the brink of death. Desmond, for his part, was experiencing something that should have killed him. So in a sense, he was in a near-death state.
The premise of "Lost X" is very simple. Everyone whose souls were not trapped on the island eventually found it impossible to move on, in a spiritual sense, on their own. The events that transpired on the island bound them together as a group; only together could they move on. While it could have been the pain and the suffering that linked them, instead it was the good moments: the love that they shared.
This wasn't imposed upon them, but was a subconscious choice. They needed to forgive each other and find closure. If it seems a bit ill-defined or vague, it's because the circumstances varied for each character, yet in the end there was also the group element. They had their individual triggers, but once they were "activated", they were aware of the totality of their shared experience. (And those moments were some of the best and most heart-wrenching moments of the series.)
This is directly linked to the redemptive themes of the series as a whole. It's not tied to a specific religion or basis of faith, though the series has always hewed closely to Christian themes. Even the characters acknowledge that "Christian Shepherd" is rather on the nose. And there are similarities to the concepts of limbo and purgatory, which some viewers will no doubt find convenient or offensive.
However, conceptually, this explains all of the inconsistencies within the "Lost X" timeline. The survivors of Oceanic 815 built a consensus reality within the afterlife that represented everything they couldn't let go in their real lives. It was the sum total of all the regrets, hopes, and fears that held them back. And as such, they had to come together in the understanding that it was time to let go of the past and move on as one. After all, all those characters were Candidates because they were alone and lost in their lives. In a very real sense, the island gave their lives meaning.
To be clear: the writers were not trying to say that the entire series was some kind of purgatory. The events on the island took place. Whatever happened, happened. But afterward, as each of the primary characters died, they arrived within the consensus reality of "Lost X". And since "Lost X" was outside of time, at least in the conventional sense, it took place both well after the main events of the story and at the same time as "Happily Ever After".
Also, considering that the spirits of the dead have been a part of the story from the beginning, this spiritual element of the story should be no surprise. If anything, the writers may have been hobbled by their own ambition. They were limited by which characters they could bring back into the story, and for how long. So while the overall effect of the message was not undermined, the details don't necessarily mesh as cleanly as they might have.
Of course, this is connected to the problem with the explanation for the "whispers" given in "Everybody Loves Hugo". Some souls are trapped on the island, but the whys and wherefores aren't explained. If Malcolm David Kelley hadn't grown up so fast, would Michael and Walt have reunited in "Lost X", along with all the other happily reunited souls? If Adewale Akinnuone-Agbaje hadn't demanded five times what he was offered to return, would he have been trapped on the island, or among the redeemed? Or is it assumed that when the Source was momentarily shut down, the souls trapped on the island were released, thus able to move on to the pseudo-purgatory stage?
But knowing that "Lost X" is really a spiritual epilogue to the main story presents yet another reason to go back and re-experience the story, to see if it stands up to closer scrutiny. Without a doubt, the writers intentionally made it seem as though there was a different origin and nature to "Lost X", so that influenced the interpretation of many sixth season episodes. With no need to reconcile "Lost Prime" and "Lost X", the spiritual and redemptive aspects of "Lost X" will no doubt seem less forced than some believe them to be now.
Also, as already mentioned, "Lost X" also served to place the denouement during the same period as the climax. Structurally, this was an intelligent choice. Had the writers tried to bring the main story to a close and focus entirely on "Lost X", even for just a handful of episodes, it never would have worked. This also maintained the narrative structure that had defined the series since the very first episode.
But it also gave the audience a season-long opportunity to say goodbye to the characters and remember all the things they loved about them from the beginning. And in retrospect, the narrative convergence of the "Lost Prime" and "Lost X" events will be even more meaningful. The conceit of "catalyzing the awakening" of each main character was a masterstroke.
That said, "Lost X" and its purpose is more than just a message that the characters themselves needed to understand and experience to complete their redemptive journeys. It's also a bit of a meta-message to the audience. This story is ended; time to move on now. Don't dwell on the negative; forgive and remember the best of what was, what was loved, what was valued, and carry it forward into the next experience. It may be a bit self-indulgent, but it is perhaps the distillation of the theme that has always been at the heart of "Lost".
Overall, this was exactly the ending that the series needed. The heart of the series was always the depth of character exploration and the redemptive theme, and both aspects carried through to the very last frame. While some mysteries were left unsolved, on the balance, the important points were all covered. A thrilling and touching end to a worthy tale.