Do you guys remember in season 1 when Locke teaches Walt to play backgammon? Locke holds up 1 black piece and 1 white piece and says "2 sides, 1 light, 1 dark". That line right there in probably the 2nd or 3rd episode set up the WHOLE FUCKING SERIES!!!1 Jacob versus Silas from Deadwood. That is brilliant writing and foreshadowing before we are really even paying much attention in season 1.
I think that by the end, we will see that the writer's had their shit together better than we thought. They had several possible events worked out before they even got the show picked up. But once it got picked up, they worked out pretty much the whole arc. There was a time late in season 2, and early in season 3 where they didn't know how long the show would be on. And that is why those episodes seem like "filler". This is the kind of show where they needed an end date to work towards. Once they found out the show would go five seasons(6 now because of the strike) things picked up and got much better. This season was an absolutely epic experience.