In honor of this evening...
I thought I would post a Lost Theory of Everything. It is still a half-formed outline in my head, however, so take it with a grain of salt. I have remained Spoiler Free this off season; going so far as to avoid watching the leaked first four minutes. I will remain spoiler free throughout the season.
The island is actually a spaceship. It is either a space ship floating in the ocean, that has grown a tropical island on top, or it is possibly the inside of the ship, a la Anathem. I like to think it is floating with things growing on top; and the ruins lead into the ship, hence Richard Alpert's additions to the truce. I believe this island is only part of a bigger ship that has either left or sunk. This ship was originally the Lost city of Atlantis. Jacob is the Captain Kirk figure. Only he has violated the prime directive. Esau (man in black) is just the holodeck. He wants turned off, or to leave, or something. Only problem is he is programed not to harm Jacob. He has o find a loophole. I have more, with evidence, but really just wanted to put down some initial thoughts.