How it all started theory
I think the two skeletons in the first season are the last survivors of the island, before giving birth to Jacob and the other guy(this can explain their non-burials).
For whatever reason Jacob and his brother, let’s say, are not getting well. Or maybe they even don’t know they are brothers. Jacob and BSG can’t kill each other because it is their fate. The island will never let someone kill the other because it will course correct at the attempt. For some reason the BSG wants to kill Jacob, I believe it has to do with an infinite loop that Jacob created.