This is an interesting exercise. What I love about "Lost" is that neither faith nor science can fully answer the questions posed by the big mystery or the characters involved. And that relates to one of the series episode titles: "Man of Science, Man of Faith." I believe that "Lost"'s aim is to conflate the conflicting concepts of destiny, predestination, faith, science, superstition, aetheism, birth, death, and rebirth and see what the result is. Can human society live by one set of principles alone? The DHARMA initiative (Dharma being a Buddhist/Hindu concept in which our actions in life determine whether or not we attain freedom in death from the eternal cycle of rebirth) appears to create an environment for these people, from which there is no escape until certain actions they perform release them (e.g. Eko) from the ghosts haunting them.
The cool thing about this show is the fact that the producers (this is speculative) must have sat down and pitched it as a science-fiction meets fantasy show. There's a little bit of Survivor in there, a little bit of Lord of the Flies, a little of The Island of Dr. Moreau, and a little Greek mythology, a little religion, a little ER, and it's all stirred up with a big stick!
What's bothering me is the dropped thread of story about the men in the South Pole (or Artic, not sure), checking the geomagnetic waves, and calling Penny. Perhaps that's the scientific aspect of it, because viewers were being led down the wrong path by too much focus on the faith/superstition aspect of the storyline. However, I don't believe the final unveiling of the mystery will be something concrete (like a golden egg in a treasure box, or a big evil man stroking a furry cat). I believe the answer will be abstract, and the true solutions of the mystery will lie in the resolution of the conflicts within each character, and the coming together of these characters once they realize that their lives are all interconnected.
I think the numbers are a massive red herring in terms of figuring out the mystery, Hurley winning the lottery was pure coincidence, and there is a powerful geomagnetic force under the earth that is regulated by the code of numbers. The geomagnetic force also explains why Des came back -- because the ocean currents only move in circles around the island, never away. As for the Others, I think they're the first generation of people who were brought to the island to be experimented on and studied. They were once just like the Losties (I guess they would be the Others to the Others if you know what I mean, hehe.) They are definitely infertile, and it may be a product of the part of the island they were brought to/dropped on. One side of the island is toxic (hence Ben's tumour), while the other side is healing (hence Rose's recovery). It's the yin-yang aspect of everything on that island.
So final conclusion: not a one ring to rule them all theory, but a larger, more layered theory about the complexity of human existence and of living together in this day and age with all our conflicting beliefs about science and god, painful past experiences, and future hopes. It's a metaphysical theory, not a concrete one. It's a thinking person's theory.