Is this the safe zone part of the FOT board where I can give my theories for season 6:
Jacob's enemy is actually the smoke monster and has been manipulating Christian Shepard and every other dead character we see roaming the island.
MORE SPOILERS
I think that scene in the finale between Jacob and other dude (maybe smoke monster? or at least on the smoke monster's side?) was the beginning of a battle for the soul of humanity. It's always been a very moral show, and the choices people made on the island both good (Charlie giving up drugs and becoming a decent person, everything Sawyer) and bad (Sayid giving into his demons) matters. It's a big chess game, or backgammon if you prefer. And I think that Jacob and other guy are either deities or something mystical, and they're in a dialectic battle over man. I don't know who believes what, but I'm guessing Jacob is the optimistic one, not necessarily good. I mean, the others claim to be the good guy, but we don't know who they follow. And the Dharma Initiative- are they just interlopers or are they there with an ideological backing?
But yeah, this show has been about a moral struggle since the start. That these people can start over, can redefine who they are, or can remain the same messed up people they were before crash landing on ABC.