The things that still sort of does bother me is that all the characters in the flash-sideways are in LA, even the ones who were never on the Oceanic flight to LA or were connected to LA at the time of the bombing. I have nothing against LA (except for the Lakers), but Dogen was from Osaka, Rousseau was French, I believe Bejamin Linus was from Oregon, etc. It wouldn't be impossible for them to all end up there--it is a megalopolis, after all--but I hope something in the main storyline explains it.
It just makes me shrug. To me it's all part of the metaphysical interconnectedness of the characters. I'm not sure it's something they need to explain because, for all intents and purposes, it can't be. The idea of interconnectedness is supposed to be a wonderful mystery, and one that's fun to ponder, not pick apart like a baked chicken.