I theorize that Jacob and the random smoke monster thing from like two seasons ago are interlinked, but I have nothing further on that.
As for his theory. It's freaking scary as heck. That means Ben could possibly do anything he wants, given resources (and yes he does have the resources, he faked the plane crash with like 300 dead bodies) and that Ben is pretty much the most powerful character in the series up to date, unless you count Jacob, and no one knows who or what he is.
Haven't they done the whole flashback flashforward thing before? Either way, it was confusing. It's always possible that Sun thought Jin died, like he got shot or something in the midst of a battle (this also explains how Kate might have the baby and Jack is hellbent on never going back.
I also guess the people who are stalking Hugo are working for Penny's dad. What ever happened to Dharma, the ring future telling lady who talked to Desmond, and the physic who talked to Clair?