<WONDERGEEK POWER ACTIVATE>
By the end of this season people are going to start coming up with uniform theories of what's going on on Lost. All there is now are ones of bits and pieces that don't connect and barely make sense a lot of times. Everything's got to come together eventually and maybe by the end of this season there will be enough information to work with.
I don't think this is hard. It just seems hard. I think the key is to stick with the main things and distinguish them from the secondary things and so on. Not everything is of equal importance. The story has to grow out of the basics. We also have to separate important things from Easter Eggs and red herrings. So what I'm doing is putting together a chart of hierarchy based on my hunch. I have a story but I won't go into it right yet.
Just off the top of my head this is how I see it. I can explain why I have things in this order but it doesn't mean I'm right of course. The further down the list the less sure I am. At this point I've heard some of the writer's commentaries but not all of them. This is a rough draft.
Primary themes............................................
yin yang
mirror matter
fate
time travel
reincarnation
time looping
immortality
course correcting
2nd............................................................
time
the "Big Clue" - there is a huge clue in episode1/season1.
changing the numbers (4,8,15,16,23,42)
the good list & passengers 'meant to be' on the island.
children (rearing,birth,recruiting)
space portals (wormholes)
the island (powers)
the island (science)
Jacob - not the man but the godlike entity.
the Black Rock
3rd..............................................................
Desmond - seems to be connected to Jacob (backwards whispers), and he's a constant.
Richard - everything about him.
Walt - I don't think we've seen the last of him.
the sickness
the Dave thing - the initial script for the episode "Dave" gave away too much info and had to be edited.
Pierre Chang
Ms Hawking
Widmore - the Black Rock connection?
Alvar Hanso - the Black Rock connection?
Abaddon
blast door map - yet to be found Dharma sites, strange stuff.
Jacob - the man.
Miles - been to the island before?
Daniel - been to the island before?
Charlotte - been to the island before?
4th..............................................................
Annie
Ben
Aaron
Locke
Hurley - can see the cabin

Magnus Hanso - Black Rock.
DHARMA
the ancients
the hostiles
Adam and Eve?
the Flight 815 pilot - who can fly 1000 miles off course?
Claire - dead? and generally creepy, she can see the cabin.
voices
visions
Hanso Foundation
Nikki & Paulo?
Horace & Olivia Goodspeed
Vincent - never around when smoke monster is.
Smoke Monster - there a real interesting theory on this the writers have given a nod of approval (not that it's correct though).
Here's a little on the "Big Clue" that the writers have said was in the pilot. Nobody knows what it is yet. We won't know until the end of the show.
these are a few possibilities people have noticed.................................
the black cylinder near Jack's head in the very first scene.
Vincent
the white shoe
Jack's pupils are dilated
Jack blacking out
Jacob? - there's somebody that looks like Jacob helping Jack with the survivors.
Smoke Monster killing pilot for whatever reason
1000 miles off course
Gary Troup - author of Bad Twin and The Valenzetti Equation gets sucked into engine.
Walt asks "is that Vincent" when they hear the monster.
The plane is in the wrong direction.
Walt is wearing white shoes.
.