So if you haven't seen last night's episode and don't want things spoiled, stop reading now.
So we finally know what this whole show is about... And its not really surprising, since they told us early on in the series (maybe the second episode when Locke talks to Walt about backgammon).
So here are my thoughts on last night's episode:
-Alpert gets one heckuva baptismal experience from Jacob. This reinforces the idea that Jacob is the good guy and The Man in Black is the bad guy.
-The exchange between Alpert and Jacob really is more telling than anything else. Jacob says that he can't absolve Alpert of his sins... But he's God.... Why can't he? Simply put, because Jacob wants people to be responsible for their own actions. If absolution of sins came for no reason, then the free will that Jacob so desperately wants people to exercise on the island is meaningless.
-The Man in Black tried the direct approach. Ask Alpert to kill Jacob. That clearly didn't work. So his next attempt... the Long con. Manipulate the people that Jacob brings to the island, to prove to the Man in Black (El Diablo) that people will choose to do the right thing, when faced with temptation, to show that people are not as good as Jacob believes they are.
-But Jacob is dead.... And now that we know the motivations behind bringing people to the island, we might understand this to be an even larger allegory of Nietzschean philosophy. God is dead. Its the ultimate test of free will and morality. Without Jacob there to provide guidance, to tell Richard how to advise the islanders, will they choose good over evil still? Or will the islanders open up Pandora's box and let smokey leave the island?
-Finally... a future hope... I really hope that Hurley takes Jacob's place. Hurley represents the everyman throughout the show. Hurley being promoted to the guardian of the island would be symbolic of the everyman being capable of triumphing over evil, overcoming themselves (Nietzsche again), transcending mere humanity into the director of their own fate and values.