My need to find a theory of everything comes from Jacob's line in the season 5 finale, which was repeated in the recap: It only ends once. What this means (I think) is that Lost-Prime and Lost-X can't be separate timelines or alternate realities - we can't be witnessing what would have happened versus what did happen because that would allow for two endings.
So this is my either very right or very wrong answer: Lost-X is actually happening (within the story) after Lost-Prime. Something will happen at the end of the series in the Lost-Prime timeline that will send them back and make it so that they never crash - and what follows will unfold in the flashsideways, which we're meant to think are totally unconnected but actually provide us with the various characters' resolutions.
Here's where I'm coming from:
- The very first detail: the mysterious cut on Jack's neck. They made too big a deal out of this for it to be a meaningless detail. It can't possibly matter within Lost-X, but I have a feeling that we should be watching out for Jack to see if he acquires a neck wound toward the end of Lost-Prime.
- Juliet says "it worked". Ostensibly, we're meant to understand that she somehow knew that Lost-X had been created, but I think that it's more than that. Recall that Desmond was similarly close to the pocket of energy when the hatch blew up, and that his consciousness was dislodged and began to shift in time. My guess is that what we were supposed to understand was throwaway dialogue - the bit about going out for coffee sometime and Sawyer saying sure - is dialogue that we'll hear her speak in Lost-X, when she and Sawyer meet again for the first time.
- Subtle character changes. Sure, Hurley saying he's lucky and Sawyer appearing to be nice are probably red herrings - it'll probably be made clear when they get character-centric flashsideways that Hurley was being sarcastic, which is not unusual, and that Sawyer is casing Hurley. But the Jack and Locke scene was weird and not easily dismissed. Locke was an angry guy before the island, but that anger seemed to motivate him. This Locke is a cynic and a skeptic - not angry, just defeated. And this Jack is surprisingly open-minded. Sure, he's tried to fix the unfixable before, but it was out of some pathological need to fix things and people. You don't get the sense, though, that the suggestion that he can help is about him.
Whether the ship/plane is itself full of despondent people or they choose to focus on them in particular and remove the rest from the field of play is up for debate - surely, the various lists play a role in this process - but the key figures in the game are all very much damaged*. As he tells Ben, the Adversary thinks that they're pathetic, whereas Jacob thinks they can be redeemed. (This is not unlike an issue of The Sandman, from the 'Brief Encounters' trade, where Dream and some of his siblings have a wager about whether Emperor Norton can be corrupted, and whether it's enough to dream.)
So my guess is that the Lost-Prime line will get dire and depressing: people will die, the Adversary will appear to win. And meanwhile, things will turn out okay in the Lost-X line and those pathetic lives won't look quite so pathetic at all. (There will be clues, too, even if they're as subtle and the Jack and Locke clues.)
Next week's episode is titled 'What Kate Does', and I suspect that Kate will do something important in both of the timelines/dimensions - it may even be the case that her story appears to end in both - and maybe one will be happy and the other one sad. Except that it only ends once. The ending she gets in Prime? To paraphrase Jacob, that's just progress on the way to hitting the reset button/bomb.
[* This is why Jacob responds to Ben's pleas with 'what about you?' Ben may be damaged, but he isn't in play, and that literally makes him inconsequential. (No one said that Jacob isn't a dick.) Except that Ben isn't, because he's still a variable and can do stuff like, say, kill Jacob - who knows whether the parameters of their game and the players they've chosen will be an issue in the end, though.]