You are all wrong.
Or, focusing on the details and missing the big picture.
You're forgetting the heavy Egyptian influence. The glyphs, statue... There were even glyphs on the counter in the Hatch (which translated into something like the Underworld/Afterlife/whatever.
The entire story is about the battle between Egyptian gods; particularly Set and Apep.
Jacob is Set - god of the desert and required chaos. Look on Wiki. The picture shown of Set IS the statue on the island; complete with Was scepter and Ankh Cross.
The Man In Black is Apep, the Egyptian God of Evil.
Richard Alper is most likely Ra.
My guess: it will be revealed that every myth has some truth, and that these guys are the inspiration for their legendary namesakes. Everyone else connected to the island - while important to the island at specific moments in time - are merely pawns in an epic and ageless struggle between Set and Apep. The island is probably some sort of power nexus - a point where our reality/this dimension wears thin. Or the opposite - it's a point that's holding things together. The universe (or multi-verse) is full of them, and there happens to be one right here on earth. A bit of science. A bit of Stephen King's Dark Tower.
What would be cool is to find out that there's some sci-fi behind this..that it's not going to turn out to be just a supernatural/Egyptian mythology explanation. Somehow Apep and Set stumbled upon the island thousands of years ago, and it's energy made them into near-Gods.
