This might be completely out of left field, but I haven't seen this raised as a possibility. What if there was a third timeline/universe which we have already seen -- i.e., where the plane did indeed crash into the Sunda Trench, neither returning to LAX nor crashing on the Island?
In "Confirmed Dead" (Season 4, Episode 2) we see the Christiane I discover the wreck of 815 in the Sunda Trench. Faraday begins to cry while watching the news, while Lapidus phones up the Oceanic hotline claiming that the plane wreck itself is inauthentic (due to the lack of a wedding band around Seth Norris's finger).
Later this mystery is somewhat resolved when we find that either Widmore had deposited the plane with bodies drawn from Thailand (according to Tom) or that Ben had staged it (according to Captain Gault).
However, what if neither was actually the case, but the crash indeed happened and was one of the possible fates of Flight 815 in an alternative timeline?
Now, I don't think this is the case, but given the importance of the timelines intersecting and possibly collapsing, and the eventuality of a merged timeline that prevents MIB from entering the world, the tantalizing glimpse of yet another possible timeline -- already noted by the show itself -- does make thing interesting.
However, given how little time is left in the show, this may well just end up on the cutting floor. Perhaps if Lost had lasted another season, the Sunda Trench plane could have been explained in greater detail.