A long while ago I registered my annoyance at 1) applying the "sci-fi" label/category to fiction that contains supernatural elements (or indeed any elements that don't have fictional science justifications) and 2) fiction whose level of fantasy or "science-hardness" is inconsistent and sloppy, which provokes the "sci-fi" mislabeling.
I still feel my "supernatural sci-fi annoyance". For instance, it hindered but surely didn't squelch my enjoyment of the "BSG" series finale (Et tu, Starbuck?). However, I'm genuinely surprised by online reviews that express the same sentiment about the "Lost" series finale. Almost from the very start, "Lost" has emphatically teased supernatural elements. As the series went on, the show contained a smorgasbord of world religions, psychics, manifestations, energy healing, power-harnessing ruins (in the vein of Indiana Jones?), immortality, prophetic intuitions. Although sci-fi stories have often ended with intricate and thinly-stretched explanations behind everything that appeared to be supernatural, it was increasingly unlikely that the writers of "Lost" would go down that path. After the episode "Across the Sea", the series finale was certain to feature a supernatural resolution. The rather bald form it took was merely an interesting stylistic choice consistent with the series' entire approach of eager religious inclusion.
P.S. my incorrect theory:
I guessed that the island was a "junction point" between space, time, and alternate universes. The island appeared to jump around in space and time relative to the rest of the world because its synchronization to it is continuously in flux. When the Monster spoke of being trapped and wanting to leave, I thought he meant that Jacob had somehow kidnapped him from the universe of the "flash-sideways". If the Monster managed to return to his own universe, then the survivors' counterparts in that universe would be in peril. Hence the warning that the Monster would "destroy everyone" if he managed to leave. Jacob's omniscience, sense of destiny, and comments about "progress" all came from his knowledge of every universe, time, and possibility. This "island knowledge" was absorbed on a much smaller scale by Locke and others, who experienced it as ineffable "guidance" because recognizing it consciously would overload their minds. In the finale, the consciousness of each of the survivors would be somehow completely synchronized and fused with their counterparts' in the sideways universe. This fusion would resemble Desmond's special ability to experience all points in time. By doing so, they would "live on" in a sense, after it became necessary to demolish the island in our universe to stop the Monster and prevent further such problems. The time traveling in season 5 was caused by the consciousnesses of the survivors working to stay in sync together as the island was "off its axis" and shifting around them. When the Six returned, they were pulled back in time to the others through the same mechanism ('course, that doesn't explain why Sun stayed in the present instead of meeting Jin...). I'm positive my theory had many holes, too, but I thought it would've made for an incredible finale.
P.P.S. my early-season incorrect theory (added May 30)
Early in season 6, my theory was that the explosion the ended season 5 had worked (recall Juliet said "It worked")...more or less. The "sideways" reality was in fact the new "actual" timeline. However, due to the island having a complicated relationship (to say the least!) with time itself, there were two complications: 1) the consciousnesses of the survivors were thrown back to an "island present" that existed in a limbo-like half-real state, 2) with the island now destroyed its malevolent god, i.e. the Monster, would finally be set free to do eeeeevil in the rest of the world. My metaphysical assumption was that the god was deeply tied to the island's very existence. The only reason the island continued to exist in "limbo" after the bomb went off was because of the Monster still being there. Once the Monster left, his presence would no longer support the island and its limbo reality, all of the events of the series would be fully undone, and the Monster would emerge into the new submerged-island timeline.
But the Monster couldn't leave until Jacob and his candidates were either dead or agreed to leave. A second assumption of mine was that in the far past, Jacob had somehow managed to trick the Monster into splitting power and authority with him. That is, in the ancient history of the island before Jacob, the Monster had been a cruel god who ruled harshly. Jacob's trick reduced him to a smoke monster who was 1) subservient to Jacob's dictates, 2) served an island role of protector and judge/executioner. (Jacob couldn't outright-kill the Monster because his own power and authority had originally come from him; the Monster would've just reabsorbed it.) By Jacob's dictates, the Monster couldn't leave until him and his candidates were gone, regardless of the island's actual destruction at the end of season 5.
In this theory, I guessed that the island would end up destroyed and the survivors' consciousnesses would merge with the sideways survivors'. Ultimately, the Monster would succeed in his escape from the island, but then the sideways survivors, who now have the memories of the original set, would confront the Monster and utterly defeat it by the entire group becoming the new plural Jacob. Meaning, the Monster's power would be siphoned off into so many people at once that it would cease to exist. In addition, I presumed that the Monster would inhabit Christian's corpse during that scene. Hence the coffin would return to "sideways" Jack just in time for Desmond to gather the whole group around to take on the Monster as it sat up.
As season 6 wound on, it became increasingly clear that my "time was rewritten" theory didn't match up, and that was when I switched to the preceding theory with the alternate universe. I spent less time dreaming up theories than many others on the Web, but in any case my impression is that everybody was incorrect in one way or another. And how did dead Sayid turn into living "apparently I'm evil" Sayid, anyway?