Yeah, I am likin' the theory that Jacob has taken over Sayid's body -- like MIB has somehow "used" Locke's persona (but not his actual body) to take over too.
So, will this Jacob/MIB rivalry continue on forever? Has it already been going on forever? (Egyptians, etc.) And we're seeing only the most recent incarnation?
That'd explain Jacob and MIB sitting on the beach last season watching a ship coming in, knowing they'd seen this all before. The modern-day version is the plane landing, and the subs coming -- people always showing up, in whatever mode of transportation they have at the time.
And Jacob and MIB continue to struggle against each other above the fray....using the folks who show up to try to outdo each other.