I think the discussion they have in the beginning of the episode about the nature of humanity is the fundamental “question” of the show.

Jacob’s enemy claims that people coming to the island always results in evil or bad things, and Jacob responds (while not directly refuting him) by saying that everything before “the end” is “progress”.

I also think the Rose & Bernard scene is an interesting extension of this thread; a moment to reflect that not everyone goes down that road that Jacob’s enemy is assuming they will; some “choose” (a concept repeated often by Jacob in this ep.) to do otherwise.