Plain and simple, I believe the writers purposefully showed us the general plot of the show way back in Season 2. The theme of 2 sides, science vs. faith, light vs. dark, etc. has been prevalent throughout the entire show.
The Hatch:
- Inside were Desmond and Kelvin
- They were both tasked with pressing the button, thus "protecting" the world, even though they didn't understand how
- Kelvin tries to leave, while Desmond remains faithful to his duty
- When Jack and Locke arrive, the two of them replace Desmond and Kelvin
- Even though Jack doesn't believe in pressing the button and Locke is the one faithful to pressing it, Locke ends up being the one to press the button
The Jacob/MIB story
- Jacob and MIB have lived on the Island for a long, long time
- MIB says Jacob is tasked with "protecting" the Island, even though Locke says its he's protecting it from "nothing"
- MIB tries to leave, while Jacob remain faithful to his duty
- Jack is generally considered the leader of the Flight 815 survivors and Locke becomes leader of the Others. Jack doesn't believe in the Island's supernatural occurrences, but Locke accepts it with faith. However, it is Locke (sort of) that ends up killing Jacob and tries to leave the island
Whether this is important to the actual story or not, it is pretty irrefutable that this theme of two people in charge of "protecting" something, both are polar opposites of each other.
I believe every season has had this overall theme, and we have carried it through to the 6th season, still with Jack vs. Locke, even though the real Locke is dead.
Lost has always been about that Backgammon game referenced in the first episode. White vs. black, Jack vs. Locke, Survivors vs. Others, Ben vs. Widmore, Jacob vs. MIB... Our version of Lost storyline vs. the "new" version of the Lost storyline...