Couple Theories...

Doc Jensen and Bigmouth have some interesting and very different takes on the finale. Here's a point from each that struck me, first up is Doc:

Last week, I speculated that in the new Lost timeline that will flow out of Juliet's detonation of Jughead, the characters that angelic Jacob visited and conspicuously touched during the flashbacks — definitely Sawyer, Kate, Sun, Jin, Jack, Locke, and Hurley — will retain their memories of the previous, now-deleted timeline. (Similar yet slightly different to what happened to Desmond after he was physically obliterated by the Swan's implosion — his consciousness migrated to the fateful week in which he broke up with Penny.)

I speculated on something like this after "The Variable" aired, only guessing that it was going to be Desmond alone that retained his memories rather than the whole group. I kinda like that idea better because it's less messy - if the entire time line changes, then when will all of Jacob's touchy-feely guys get their memories back? Will they have them from birth? Will they just suddenly remember (like Desmond did of Faraday's message)? Or will their minds be transported to their alternate time line's bodies ala Desmond in "Flashes Before Your Eyes?" If they do end up retaining memories, I think the latter is the most plausible way. Of course, when in the time line they end up is solely at the discretion of the writers.

But the big problem with changing the future in general is that it would also likely negate Jacob's death. If Flight 815 never crashes, there's no loophole for Jacob's Nemesis either (unless the Island is somehow immune to the time change). Why the heck would they even want to go back if they know Jacob is still alive and Jacob's Nemesis' motivation is thwarted? This fact alone makes me think Jack and crew caused the Incident rather than negated it. Plus, if "they're coming" means Jack and company are being transported back to 2007, then it seems likely time didn't change.

Bigmouth has the same sort of problem with this:

Nothing we've already seen on the show has changed as a result of detonation of the Jughead's fission trigger. Flight 815 crashed on the Island just as it always did -- there is no reboot yielding a grandfather paradox. If that's where the show were going, I believe we would have received some small but clear indication of its direction. Something like Cort's horn -- those of you familiar with the Stephen King's Dark Tower series will know what I mean. Instead, we got just the opposite in Miles's sardonic comment that Jack and Co. might be causing the Incident by trying to prevent it.

By that same token, it's equally wrong to say this was all simply a case of whatever happened, happened. I maintain that our Losties, like Desmond, changed what was supposed to happen. It is this altered timeline, in which they save the world, that we've witnessed thus far. Because neither the Incident nor activation of the Fail-Safe was supposed to happen, the general rule of course correction doesn't apply. Both events must thus be actively preserved. If anything changes, as Ms. Hawking said, every single one of us is dead.

In other words, the reason all this happened is because now they're supposed to be transported back to 2007 and save the world from Jacob's Nemesis. Yes, they caused the whole situation in the first place (likely because of Jacob's Nemesis' machinations behind the scenes), but because Jacob visited them all in the past, he set up a loophole of his own so they can make everything right again (and possibly get himself resurrected in Frank's body). Erasing the fact that Jacob gets killed is the biggest problem I have with the changing the future scenario.

And one last point to chew on - we know Desmond still "has a role to play," according to Eloise, and we know he's going to end up back on the Island at some point (in order to tragically break his promise to Penny - you know the writers wouldn't have set that plot point up for nothing). So if all the Incident Losties do end up back in 2007, how does Desmond get back to the Island? What motivation is there for him to go and what will he have to do when he gets there? I'm guessing that Desmond is so important that Jacob's Nemesis tries to kill him and his family, so Desmond goes back in order to protect Penny and Charlie and plays an instrumental role in the Nemesis' defeat.

That's my theory for the moment anyway. I'm sure it will change 27,000 times between now and next year. :)