I don't know where to start so this will be random.
1. I don't think MIB is Esau. If it was I can't imagine why they wouldn't just say it. I'll be REALLY annoyed if his name is Bob. Bob the smoke monster.
2. I too am confused with whether he died or what. I think that the MIB is really gone and the one we've grown accustomed to is purely the smoke monster. If there was some part of MIB in smokey, then I would think some part of John would be in Flocke? Or is it just all of his memories, or maybe since MIB became the first thing smokey jumped into.
3. The good vs evil thing is annoying me too. Obviously neither of these people are purely good. Jacob may be purely evil I guess. He's a whiny little brat at the very least.
4. What the heck is the light? Is the island like the garden of Eden or something? Smokey being the serpent?
5. Was "mother" a witch or something? How did she know what she knew? How did she make it so they couldn't kill each other, yet it appeared that Jacob killed MIB.
I think I'm more confused now than ever. I'm going to hold on to my epilogue theory though, it's the only thing I have left!