This may seem a bit late, but it's something I actually wrote back on 5/31/2010, shortly after the show ended. I'd posted it to another site at that time.
First, a few observations.
At the vending machine with Sawyer, Juliet said you can unplug it, then plug it back in, and technically it's legal. The candy bar next to the Apollo bar was called an Avalon bar.
Jack's appendix scar is more interesting than I first realized. It first appears as an out of place anomaly after the flight lands safely since they devoted a whole episode to the fact that it had to be removed on the island. Then, once you realized that the alternate timeline is purgatory, you might notice two more things. One is that since this is all after Jack has died, it's also after he's had his appendix out and so it makes sense that the scar would be there. But also, like the bleeding scar on his neck, the appendix scar also happens to be where Smokey stabbed Jack, and it's what killed him. Then there's an even deeper secret, why did Jack get sick and have to have his appendix out on an island that cures illness? For the same reason the Locke had to lose his kidney. Jack was eventually going to be stabbed in that spot and if he still had his appendix the wound would have killed him rather quickly. But Jack had to be able to survive the fight long enough to climb back down to the heart of the island and plug it back in.
In the last season finale, we saw Kate touched as one of the candidates selected by Jacob. But then we don't see her name ever with the other candidates, then we're told her name was crossed out and Smokey doesn't even need her. I kept insisting that Kate had an intrinsic role to play, perhaps as a Trojan candidate. Well who killed the smoke monster? It was Kate. That's why she had to be there.
In Ben's secreter room, behind the hieroglyphics door, was a pool of water. Ben pulled a “plug” out of the center of the pool and the water drained out. This was how Ben summoned the Monster (or thought he summoned it). Like a miniature heart of the island.
Lost: the Literal Theory
I started calling this the Literal theory because I wanted a theory to explain things literally, not just figuratively as many people are looking at the show now. So this is my theory of literally what happened. There's still a fair amount of conjecture to this theory, but those parts aren't the important parts and I'll be pointing them out anyways. This idea stems from accepting a few key concepts to Lost. One is that as the directors always insisted, there is a science fiction explanation possible for everything (as opposed to a simply magic explanation, or no reason explanation). The other concept, which follows somewhat from the first, is that everything we've seen happened literally (except for the alternate timeline, which was purgatory, but still important to the overall idea of the show).
Let's start at the beginning. And by beginning, I mean our glimpse back at the most original, oldest thing of the island – the pool of radiance at the heart of the island. The key detail to me is that what we saw was clearly man made. The most basic source of all the island's mysteries isn't some group of magic crystals or a miniature sun or anything that we might say is in some way natural; it was an arrangement of human worked stone constructions.
And I don't think there's any more to see, like we were getting more cover-up and what was really the source of the island was below in the corked up lava area or anything. I think we've seen all there is to see. And if there was more I can't exactly imagine ancient humans constructing this chamber out of stone in the middle of an electromagnetic hurricane, or wading through lava to wall off an erupting volcano. Add to it Juliet's line about it being technically legal to unplug the machine and then plug it back in again. This is clearly meant to reference the heart of the island, and draw a clear parallel to the operation of a machine.
So I'm deducing three points here. One is that the island and what it does is analogous to a machine. The second is that the machine isn't just some mundane machine manipulating an unbelievable energy. The closest we've seen to that is Smokey constructing his wheel. The wheel could be considered a mundane machine manipulating an unbelievable energy. The machine is the source and cause of what the island does. The third is that the ancient humans who built the chamber would have had to have had help building it. Brilliant modern physicists don't really understand it. The one person who may have been most intuitively in tune with the way the island works, and most understood it (Smokey, he was special, and this was one of the ways), could only figure out a few ways to tap into and manipulate the actions of the island.
This part is a bit more conjecture, but I'll explain why I think it's this way. Again, the people who built the heart of the island were just basic tool users. There's no way they could figure out how to make what the island does without knowing more than we do about math and science and physics. It's like the ancient Greeks building radios without having any understanding of electricity or advanced metallurgy. I believe the builders had outside help. What early humanity received was a great gift from a higher power. This higher power either constructed the difficult and necessarily advanced parts of the machine and the humans just built the control interface that they'd be able to wrap their heads around, or the higher power directed the humans how to construct this machine using the tools and techniques at their disposal.
I'm leaning towards an assumption that the higher powers who helped humanity were non corporeal beings who resembled a living cloud of black smoke, just because that'd be a fitting explanation of why someone might be transformed into this sort of being. They might have been aliens from another planet. They might have been transdimensional beings (kind of like the “aliens” in Indiana Jones and the Crystal Skull). Heck, they might have been flesh and blood aliens that looked like the statue of Tawaret. They might have interacted with us directly, or they might have only communicated with us from afar. Considering time travel was something they were capable of, they would have been a pretty transcendental, higher power.
But what they gave to humanity was an afterlife engine. A machine that manipulated and recycled electromagnetic energy so that everyone and even every animal on the planet had a little ball of electromagnetic energy inside them that acted like a copy of their mind. And, at least as it was currently set up, when people died the electromagnetic copy of their self migrated to the island where it could go on living a life of sorts, sorting out and dealing with everything it couldn't in life, and even using a time travel ability of the afterlife engine to interact with those who went before or went after whenever that might have been, and keep going infinitely until they're ready to let go.
The effect of this engine is meant to be as unobtrusive and non-interfering as if it wasn't there at all. But just like in quantum mechanics where you can't measure something without interacting with it, there were occasional side effects. Walt's ball of light could somehow interact with the ball of light in animals and sometimes with other humans. Miles could tap into people's ball of lights after they died and it was no longer recording, but before it had left for the island. That's how he could hear dead people like they were broadcasting their last thoughts. Isaac of Uluru could tap into the engine's self repair ability that normally only extended to the island space and make use of it. Faraday used modern technology that could directly impact the ball of light and affect it's innate potential for time travel. The psychic Malkin also tapped into a ball of light's potential for time travel and accessed bits of knowledge from it's future. The island itself too was meant to not be an outside influence, and as much as possible was removed from the face of the earth.
It's possible that the rules the engine follow might be controlled by the guardian. It's possible that under Mother the engine was a reincarnation engine, where each ball of light was immediately re-put into use without access to the memories of its previous lives until it again returned to the island, creating a sorta wheel of karma. Or as Mother would have put it, the same things keep happening and it always ends the same. Jacob may have altered the innate function of the engine, giving us the concept that we have today. It only ends once, and everything until then is just progress.
The engine was damaged, though. About 30 years ago an atomic bomb was detonated in part of the engine's machinery. Most noticeably, the ability for the engine to connect to babies conceived on the island was messed up, killing the mother and the child. The atomic bomb might have had other effects as well. Perhaps it removed some of the safety features and allowed Faraday's research to work, or that may even have been the source of Walt and Miles and Malkin and Isaac's powers. Slight hiccups in the functions of a few people's ball of lights. I hope that the engine is self healing, and given it's time traveling nature, I would assume it is. When it comes to the obvious controls, I think the engine was meant to be plugged in and never monkeyed with again.
What about the unanswered questions?
Without getting into every little unanswered question, I think I can explain why so many details were left unanswered. I always assumed that the end of the show would leave some aspects up for interpretation. That's just the shows style. Another person indicated the “Midichlorian Effect”, when a character announces on screen an explanation to a mystery that we the audience had come to accept as simply being mysterious and are ultimately let down by the explanation. Sometimes we're happier just not knowing.
Some mysteries simply resulted due to production reasons. If you noticed, young Smokey was special, Walt was special. Young Smokey seemed to come across knowledge magically, Walt had knowledge come to him magically. The game was between two players, one white and one dark. Young Smokey could see and commune with ghosts that other people couldn't see, Hurley could see and commune with ghosts that other people couldn't see...
Walt was originally intended to have the final role that went to Hurley. He was being set up for it, and the whole three year gap was built into the show specifically to let Walt back into the cast. The problem was that Walt grew too much as a person, and didn't grow enough as an actor. So they had to shift his role over to another character. I'm sure there are numerous examples of side story lines being started then later abandoned.
The biggest nugget of interconnected mystery, however, is the DHARMA Initiative. Who's side were they one? What was Alvar Hanso's deal? Where did they go? Who found the island using the computer room Eloise took over? Etc, etc. Even the numbers and the nature of the smoke monster are tied into their mystery. And it's not like the producers didn't put thought into what these answers might be; they put a lot of work into the Lost ARG's concerning the DHARMA Initiative. In fact, I think they put enough thought into background information and unanswered questions to create a DHARMA Initiative based Lost spin off. I think that's a big reason behind all the unanswered DI questions.