It would be easy enough to delete Season 2 completely. That whole season is basically "OMG the tail section!" which ultimately becomes useless as pretty much everybody except Bernard gets killed.
You'd have to introduce The Others immediately, and anything having to do with Jacob or the Man in Black would probably have to be deleted.
What's funny to me is that, while playing the new Tomb Raider game, all I kept thinking the whole time was, "This could totally be the island from LOST."