- Maggie Grace's (Shannon) absence from the beginning of the new season will be explained by a significant change to Shannon and Boone's (Ian Somerhalder) backstory.
This one is interesting.
If both Shannon & Boone were not on the plane (or in the first episode)then the change to the backstory could involve Shannon's father not dying (ie, Jack saves his life, but not his future wife's), so she never "runs away" or hooks up with that guy in Australia so they would never try tricking Boone into giving her money and traveling down under, so they both wouldn't be on flight 815.
But Boone is on the plane (and in the first episode), but Shannon isn't so something else must happen.
What, I'm not sure.
The easiest way would be to just say, Shannon never left Australia with Boone in this timeline, but rather ran off with her boyfriend, or maybe freaked out after sleeping with Boone and caught a different flight, or got kicked off the flight before take-off for being a bitch, however it happens, it ends up with Boone traveling on 815 alone.