Please do not read the following if you have not read Replay by Ken Grimwood, unless you have no intention of reading it. This post has a lot to do with that book, and I found it a moving story which I'd recommend. So, fair warning, then. Read on if you'd like.
(Oh, and apologies if you have read it. Some repetition below.)
I just finished reading it, actually; and, since it deals with time travel through a loop, I got thinking about Lost. The difference is, in Replay things can change each time the loop starts over. The big events remain the same, as they have in our own history (Kennedy assassination, Vietnam War, etc.), but events of personal history can change. The two main characters benefit from foreknowledge of major events, but cannot "predict" anything else, beyond helping a couple friends escape some personal sorrow. Still, they live the loop over and over.
At first, they each think they're the only one replaying. Then they find each other and it's like they're not alone anymore. They understandably become close, as they're the only people they've met living this way. Eventually, though, something drives them apart. They reconcile in another replay, but not perfectly.
That's not the way it ends, but it got me thinking: this is the "many worlds" interpretation of a certain aspect of quantum mechanics, with the twist being two people keep reliving portions of their lives through many of these worlds, wherein most of the events remain the same. Their lives change drastically each time, but they keep starting over. And after they meet each other, they remember in their subsequent lives.
Once, they go public. It turns out bad when they "predict" events, because people think they are psychic. But they're not really predicting anything. They just remember the important things.
So, all that to ask: what if Jacob and the Monster are like these people? What if they are looping through lifetimes, through timeline after timeline? I guess it would sort of make them the Constants of all timelines - which could be a clue as to why we're watching this other timeline. Maybe "It only ends once" means it only ends when all timelines end, instead of each individual one.
Being the only two going through this, perhaps they had been close once. Obviously that's not the case anymore. What if the conflict between them is a difference of opinion about whether they should influence things since they know so much? They may have joined forces and tried to do just that in a former life, but failed with drastic consequences. Maybe one of them thinks they can stop the end, or fix some problem, and the other doesn't.
I know it's out there, and I actually don't really think it's one of the more probable theories. But I don't really think that's the point of theorizing about Lost. I just like to discuss ideas like this. So, what do you think? Go ahead and poke holes. I know they're there!