I think the alternate timeline may in fact be a flash forward.
My theory is that that MIB succeeds in destroying the island, and uses it's power to set up an alternate reality where he can experience the life he always wanted in the outside world. He used the lights power of rebirth to reconstruct the world and bring back the people that died, giving them all what they wanted in an attempt to keep them happy and less likely to remember what happened before.
-It is obviously significant that MIBs name has not yet been revealed, and also that Davids mother has not been shown. Therefore I believe that MIBs name may in fact be David, and his mother may turn out to be Jacob's/MIB's mother.
-Unless I am forgetting something David is the only character that did not exist before the alternate time line started.
-MIB wasn't a bad guy when he was human, he just didn't want to be stuck on an island his whole life... and after 2000 years I can't really blame him for going through any means necessary to get his freedom.
-At the beginning of s6 the island is underwater. This has bothered me most of the season, since if the island is underwater it implies the MIB is not on it, and life has gone on. Also setting off a nuke would not sink an island.
-Desmond's flashes have always been through time, why would he be jumping between dimensions now?
-I am not sure why but the fact that Christians body is still missing is important, but I am sure an explanation could be found that fits into this theory.
-There are still a couple things I have yet to fully fit into this theory, like why does everyone keep implying the world will end if MIB escapes... could this just be an assumption since Jacob's island protector tutorial didn't exactly seem to be comprehensive?
-I think at the concert where David will be performing the truth will come out and the final showdown will happen, though I have no idea how it will play out.
Thoughts?