[Spoilers follow for those not caught up to the current episode of LOST!] [Although, if you're not into LOST, none of this will make any sense to you but I think my final paragraph explains why I like it so much.] [So read the last paragraph if you want to know my argument for why you should watch LOST!]
Now that we're halfway through the final season of LOST, some things are actually starting to make sense. Actually, the turning point seems to have been the end of Season 5, when we are finally introduced to Jacob and the Man in Black and everything starts to fall into place. Some have complained that this is a deus ex machina because these are supernatural figures that can do some very unnatural things (although there are clearly rules that limit what they can NOT do as well!). But it's not a deus ex machina. For one thing, the Man in Black has been seen since the very first episode as one of the major mysteries of the island. Also, Jacob has been referred to by name as far back as Season 2. The complaints that the mysteries of LOST are boiling down to a "Jacob did it" kind of explanation are glossing over the whole theme of the show: not faith, but science and faith. The complaints are missing the significance of the Dharma Initiative and the parallels with Jacob.
One major question I've had about Dharma is why they were allowed to stay so long on the Island and do so much when they were obviously exploiting it and feuding with the natives. (And what changed when they were purged after, what, 20 years?) I think a major window of this was opened when Jacob talks about why he brings people to the island: to observe and see what they will do. Obviously, Jacob is a kind of god, but that describes his power, not his motivation. Jacob's motive is to test and experiment (with humans, because he doesn't have to go through an IRB ... ). Jacob is a scientist at heart.
So, Jacob would tolerate the 70's wackiness of the Dharma Initiative, partially because some of them are candidates, but also because he can't exactly condemn them for wanting to experiment when that's what he's doing all along!
A lot of people have been pulling out parallels to Season 1 but I think Season 2 is more parallel. There you have the debate about whether The Numbers in the Swan Station mean anything or are just a cruel trick, an experiment. The answer is they do mean something. After Locke loses faith in the experiment (aided by Ben), Desmond has to step in and save the island with the failsafe key. And now, Desmond has shown up again, just in time for the end of the show.
So does Jacob mean something/can he be trusted? Well, despite Locke's doubts, the Swan Station meant something. So I'm inclined to believe that despite the Man in Black's claims that the Island doesn't mean anything that the Island itself is indeed very important, and that Jacob, for all his hands-off scientific behavior, can be trusted. At least more than the Man in Black!
What this means is the whole show is about knowing and doubt, and about science and faith. The Dharma Initiative is the exploration (and exploitation!) of science, and Jacob is the symbol of faith and trust in the midst of doubts. The thing about LOST is that both Dharma and Jacob are part of the story, just as science and faith are part of life. I've sensed this subliminally for a while but now I think it's coming together. I'm still not sure if the ultimate resolution will be worthwhile -- I suspect that the author's own philosophy may needlessly color the show's conclusion -- but I can say, halfway through Season 6, that there has never been a show like this and probably never will be again: a show that is about an entire philosophy that relates science and faith, a true "mystery" show told as multiple rich narratives with fun sci-fi fluorishes. If you want to know why you should watch LOST, that's why.