The flashbacks were not the original time line but the result of Jacob/MIB interference by Leyla79

This theory presumes that the plane lands safely in L.A. and there is an alt time line presented. If an alt time line is presented, I believe that it will in fact be the original time line for these characters, and everything we have seen play out in seasons 1 to 5 is in fact an alt time line that is the result of Jacob/MIB manipulating events, from who got on the plane, to the crash, to the time skipping, to the six getting off the island, to the five coming back, to the nuke, etc. One example of how this worked - Sawyer was writing his revenge letter and only finished it because Jacob gave him a pen. Without that pen, the letter would not have been finished. Sawyer carried that letter around and became a source of obssession for his revenge. This undoubtedly framed his entire existence, and ultimately was the reason he got on that plane. Take Jacob out of the equation, Sawyer's life would be very differe! nt.

The characters from the nuke site flash forward to 2007 and find out that they are stuck in some weird time loop paradox that exists to prevent the occurrence of a tragic event that has major implications for mankind. Jacob created this paradox as a means to prevent the tragedy from occurring. If Peter Griffin can bring world peace by going on a date with Molly Ringwald instead of Lois, then making a plane crash with random people can stop the world from ending. The new alt scenes will be used to unveil why each main character was ultimately chosen for this purpose - so we will see in the original time line the role each played that may lead to this tragic event. When the characters find out that their lives as they know them are not the lives they were supposed to live, but yet this paradox is necessary to prevent some tragedy, they will be forced to choose whether or not to remain on the island stuck in that paradox OR to somehow undo it and let nature take it's natura! l course. The war may ultimately be one between Jacob, who believes man is inherently good and that the paradox needs to continue to exist, and MIB, who believes man is inherently bad and wants to undo the paradox to allow this tragedy to occur, but it will ultimately be the decision of the main characters.