Q: Why can't Jacob or the Man in Black kill each other?
A: Because it goes against the rules that Jacob made. He gets to make these rules because he's protector of the island. How exactly these rules work isn't known. The only hint we get regarding the nature of the rules is a scene where Jacob/MiB's mother stops in her tracks, looks at them, and says, "I've made it so that you can never hurt each other."
Why it's stupid: The entire foundation of the show hinges on the audience's ability to buy into these mystical rules that don't have any sort of logical backing. Without the rules, the conflict of the show wouldn't exist. That's the only reason the writers included them. Aside from that, they're not important, and the writers spend about ten seconds total dealing with their inclusion. In any other show, viewers would flip off their TV screen if writers tried to justify a plotline with unexplained "magic rules". In Lost, it's considered par for the course.
Q: If the losties created the alternate reality in the afterlife as a way to remember and to let go, why does Desmond's consciousness jump there? Why was that necessary to make them remember? What would have happened had his consciousness not triggered in the afterlife?
A: Who knows. I assume that all of the losties would have eventually remembered anyway, seeing as how that's the only reason the alternate reality existed in the first place.
Why it's stupid: By making the alternate reality the afterlife, Desmond's significance in the story is nullified. He's been built up since the second season as a man displaced from time and space, but that subplot hadn't yet served a purpose in the overall narrative. With the series finale, Desmond's journey is rendered irrelevant. The only point to his consciousness-altering state was so that the writers would have something cool for his character to do.
Q: What point were the writers trying to make with the show's central themes (fate vs. free will, science vs. faith)?
A: They weren't.
Why it's stupid: Generally, themes are supposed to have some sort of purpose. Otherwise, what's the use in having them? This is the question I find myself asking over and over when thinking about Lost's themes, and the answer I keep coming back to is: there is no point. The writers assumed simply having them was enough. They never bothered to figure out what they were trying to say, or if they even had anything to say.
Q: Why does the smoke monster get stuck looking like John Locke?
A: Because Jacob died. Apparently, if the protector of the island dies, any smoke monsters on the island are no longer able to change form. (Unless of course it's to revert back to their smoke state, in which case it's totally fine.)
Why it's stupid: The writers needed an excuse for why the Man in Black would stay looking like Locke, so they came up with a throwaway line to facilitate it.
Q: Why does Ben not recognize any of the losties from when he was a kid?
A: Because he gets amnesia after Richard heals him.
Why it's stupid: When in doubt, give your characters amnesia. (24 taught me that!)
Q: If Christian was actually the smoke monster, how was he able to appear off the island? Why did he get Vincent to wake up Jack in the bamboo forest? Why did he lead Jack to water? Why did he say he could speak on Jacob's behalf?
A: Maybe Jack was hallucinating! Maybe the Man in Black was bored! Maybe he was lying! Maybe it all part of his plan to get Jack to trust him, and he just never got a chance to take advtange of all his hard work!
Why it's stupid: Maybe--just maybe--the writers were making it all up as they went along.
Q: Why does falling into "The Source" turn you into a smoke monster that sounds like a machine and judges the lives that people have lead?
A: It just does, ok?
Q: Why did the writers keep Sun & Jin separated for multiple seasons, only to kill them off almost immediately after they were reunited?
A: Because they're d*cks, and they had nothing else for them to do.
Q: Why can't Ben kill Widmore? What are "the rules" he refers to?
A: Oh wait, he can kill Widmore, and he does. "The rules" only mattered before, when the writers needed them to.
Q: What's up with Walt?
A: He's special. End of story.
Q: If the reason the Others dressed in rags was to fool the losties (for some reason), then why did they bring kids along with them?
A: Because the writers had no idea who the Others were until later, and hoped that nobody would notice.
Q: Wasn't it awesome when the Black Rock rode on that giant tidal wave and crashed through the four-toed statue and ended up in the middle of the island?
Q: OK, you've made your point. Can you stop now?
A: No, f*ck you.
Now here's a brief sampling of things in Lost that seemed like they were significant in some way, only to subsequently be revealed as having no substantial bearing on the narrative:
1. The entirety of Season 5. They left the island, came back to the island, skipped through time, lived with the Dharma Initiative, and for what? So you'd be mislead when the writers introduced the alternate timeline in Season 6.
The entirety of Season 4. An excuse to throw some new characters into the mix, none of whom mattered.
Widmore. Built up since Season 2 as being this mysterious villain, only to show up randomly in the final season and then get killed off without actually doing anything. Apparently Jacob talked to him at some point and he changed his mind and came to help protect the island. M'kay.
Eloise Hawking. Built up since Season 3 as this mysterious figure who knows a lot about the island, has a complex understanding of the fates of the characters (particularly Desmond), and is portrayed in a manner that would suggest she has some grand importance in the story. Nope, nope, and nope.
Illana, Caesar, Dogen, and Abbadon. Four mysterious new characters who were built up and then killed off when the writers didn't know what to do with them.
The Temple. Built up for several episodes during the beginning of the sixth season. Nothing comes of it.
The Numbers. They were cursed. Dharma used them. Jacob identified the candidates with them. Why? Don't ask, they're not important.
The Sickness. I still have no idea. Rousseau may or may not have been infected with it. Claire may or may not have been infected with it. Sayid may or may not have been infected with it, but then Desmond gave a speech about love, and then he may or may not have been infected with it anymore.
The bird that said Hurley's name. Guys, seriously. A bird. Said Hurley's name. Twice.
But don't let any of this convince you that the writers had no idea what they were doing with the story. After all, the Adam & Eve resolution sure panned out, huh?
There were certain things we knew from the very beginning. Independent of ever knowing when the end was going to be, we knew what it was going to be, and we wanted to start setting it up as early as season 1, or else people would think that we were making it up as we were going along. So the skeletons are the living — or, I guess, slowly decomposing — proof of that. When all is said and done, people are going to point to the skeletons and say, "That is proof that from the very beginning, they always knew that they were going to do this."
SOURCE: Entertainment Weekly
Three years later, here's their response in an interview with Alan Sepinwall from Hitfix.
You've said many times that when people find out who Adam and Eve are, we'll all realize just how long you've been planning the mythology. Well, I went back and watched the "House of the Rising Sun" scene, and Jack says that the clothing looks like it's 50 years old. Is he just not very good at calculating the rate of decay on fabric?
CUSE: Jack is not really an expert in carbon dating.
LINDELOF: He's not really a forensic anthropologist. We need to bring in Bones.
CUSE: Or Charlotte. She's an anthropolgist.
LINDELOF: The other theory that I would like to throw out there is that Jacob and his mother were just expert craftsmen. They made those clothes on that loom so well, it would appear that they were only 50 years old in decomposition, when in fact it's several thousand.
CUSE: Or perhaps the fabric is magic. A lot of theories there, Alan.
Like I said: Poor storytellers, excellent bullsh*tters.