After 4 months of pondering, reading, researching, and more pondering, I've finally come up with my conclusion of what I think will happen.
The explosion of the bomb changes the Losties past. They suddenly find themselves back in their past, possibly September 21st, 2004, with the memory of what had happened (would it be a good final season if the last 5 seasons were wiped from the characters minds?). Any characters who died would be back, because they never died.
I now draw your minds back to Course-Correction. First explained in the Season 3 episode 'Flashes Before Your Eyes'. Eloise Hawking explains to us that when someone changes a future situation, the universe course-corrects itself so that the situation will present itself once again. The prime example would be that Charlie was meant to die, and Desmond had to keep on saving him and the universe kept on having to course-correct itself.
Jack, using the knowledge he learned from Eloise Hawking's son, Daniel, used the bomb to change the past. However, I believe the rules of course-correction still apply. Just like when changing the future, major events will present themselves once again. Because of that, the Losties will eventually end up on the island again. All of them were meant to crash onto the island, and even if they've changed the past so that Desmond can't blast them out of the sky, they will eventually end up on the island. Maybe Oceanic Flight 815 crashes for another reason. Perhaps they land in LAX (hence the season 6 premiere title), but they will all have to return to another plane because the universe course-corrects itself (giving Oceanic their 'perfect record mentioned in a certain commercial'). In any case, they will all end up on the island alive, because that's what was meant to happen.
Now, will they crash on the island in 2004, or in the 2007 timeline? I prefer the latter, because of Jacob's last words They're coming. It also would make sense that Jacob touched all of those characters to 'draw them' to the time of his death. Or maybe his touch gives them some other protection of sort, who knows. I like to think of my theory as 'flexible'.
We'll assume for now that they travel to 2007, in one way or another. Now, I want to be clear. Any time-changing Jack and co. have done, has already been in place for the 2007 group. They're in the future (technically), so they would have already experienced any changes. If there was a specific point where they jumped from original timeline to altered timeline, it would be during the flash on the plane, because they jumped from late night 2008 to a brisk 2007 morning. Need proof? The pilots hear the numbers playing on the radio, the same numbers Rousseau turned off 19 years ago, replacing it with her message. Unless someone from 2005-07 decided to put them back on, this is a small difference between the original and altered timeline. Changing the message isn't that important of a detail.
Then, further course-correction will take place. All of the characters who ended up dying would eventually die again. Boone was meant to die, so he somehow will. Charlie will be back, but will die of unforseen causes. This would explain why so many past cast members who've died (Boone, Charlie, Shannon, Daniel, Juliet, etc) have been asked about returning to the show as guest stars. They would only appear for a couple episodes, however, because they all would eventually die. Unless of course, someone attempts to avoid course-correction successfully. That could be another Whatever Happened Happened vs. Change the Past debate.
Now that the time-change has been addressed, all of the right characters are alive, and they're all in the same timeline, Darlton can now forward the plot to dealing with Unlocke/Nemesis/MIB and solving mysteries like the smoke monster, Adam and Eve, and why Rousseau developed an eastern-European accent over the course of 16 years.
I'm pretty sure this ties in with many different conclusions. I think it sort of bridges the gap between Changing the Past and Whatever Happened Happened. Comment away, fellow Lost fans.
And for anyone who firmly believes the Grandfather Paradox... the day before you kill your grandfather, Jacob comes up to him and convinces him to donate to a sperm bank, which your grandmother uses to give birth to your parent.