Religion vs reason: the battle for control of people’s minds/lives, the acceptance/rejection of God, moving on from religion/superstition. The island is a metaphor for the mind. It is a place where these opposing memes do battle for control.
Religion:
• Headed by Jacob
• Jacob interferes with people’s lives and causes huge changes and problems that are extraordinarily difficult to solve.
• Jacob doesn’t appear to those who are working or otherwise engaged. He typically interacts with children and those adults in distress (see “the incident”. Hurley, the uber-innocent is the notable exception). This is true also of religion.
• Jacob was not concerned about his death since he is religious.
Reason:
• Headed by MiB
• MiB’s alternate form is the smoke monster, which is a metaphor for the way reason/lack of belief appears to believers.
• The smoke monster “kills” those that lose their faith permanently. Perhaps the pilot prayed as the plane was crashing and lost his faith upon regaining consciousness in the jungle and realizing what happened or maybe he was just never a believer.
The alternate reality shows what would have happened without the game being played at all. It is so far completely bereft of religious interference and everyone is healing themselves without the aid of a God. This foreshadows the endgame where MiB wins and religion is left behind to the benefit of mankind.
The button of season 2 illustrated this theme. However, it was portrayed as though pushing the button was an act of faith, when in fact it was an act of reason. Desmond and others interpreted it as an act of faith, because they were ignorant of the facts of electromagnetism. This demonstrates what God is--a stop-gap in our understanding of the universe. Jacob is ultimately doomed to failure as science/reason probes deeper into the depths of human ignorance ala the Dharma initiative.