The ultimate LOST theory:
You had a caretaker on the island (may have been Adam or Job or someone we've never heard of) and you had the smoke monster(aka the Devil/evil) on the island. Esau forgives Jacob... they become friends again as in the bible and arrive on the island. The smoke monster tricks Esau into going down the dark path and killing the caretaker, he does.
So we get skeleton #1 with the white stone... Jacob becomes the new caretaker and has to kill his brother Esau to keep the evil on the island... so we get skeleton #2 with the black stone.
Now the smoke monster/devil is taking Esau's form... notice Jacob never calls him Esau because he is no longer his brother. If the balance of good vs evil should ever tip to evil the smoke monster would be unleashed on the world.
So what's the deal with the flashsideways/alternate timeline. Well this is a world where the evil escaped the island. Things are about to get very, very bad.