Okay. Here's how I see it. Forgive me if a similar theory has been posted. I, personally, haven't read one exactly like mine.
Obviously, Evangeline's whole "soul memory" statement is important: the fact that in the alt they "remember" things, like the appendix, the cut on the throat, and the whale doll. So clearly, there's a connection between the two timelines. Like a thread. Or, as I see it, a river.
Think of the separation between the two timelines (a separation that exists in time and space) as a dam blocking that river, keeping the two separate. But every once in a while, there's a crack in the dam, and a little tiny spurt of water gets through, these being those "memories" our characters have been suddenly remembering. It works the other way too. For example, Juliet said "it worked."
The point of LOST is the characters. Events are important, but it is more about their issues and their redemption. And thus, they most likely will find redemption. However, I believe that, however redemption occurs, it doesn't necessarily happen in the original timeline.
What's most important about LOST, however, is the relationships AMONG the characters. How they relate to each other in relation to their own issues. It’s not just about intrapersonal exploration, it’s about interpersonal development.
I think that, due to some cataclysmic event or other, due to either the mythology or science of the show or both, at the end of the series, that dam is going to break. Also, all the characters will die on the Island. By the end, they'll all be gone.
When that dam breaks, the original timeline doesn't matter anymore. They're all going to die. Possibly there might even be an "end of the world." However, because the dam breaks, all of the memories from each timeline transfer to the other. Everyone in the alt remembers everything that happened to them in their other life. This is important not because of the events that happened to them, necessarily, but because of the people they met. They will suddenly all recognize each other. They will remember. All the relationships they formed will be there (because it's destiny). And, because the show is about LOVE, that is what will ultimately be important. The crisis of the Island will be surpassed in the alt, because it didn't happen. The original will be gone. But they will remember everything that happened, and the people they grew to love. They'll all be together.
Sun and Jin. Jack and Kate. James and Juliet. Locke and Helen. Charlotte and Daniel. Miles and probably Ana Lucia in the alt (speculation that she's his mysterious girlfriend). Sayid isn't married to Nadia, and he'll return to Shannon. Hurley and Libby. Charlie and Claire. Ben will have a meaningful relationship with Alex. (Seems that Boone and Michael would be left in the cold, assuming Michael’s even important in the alt.) They'll all be together, as they were meant to. Because it's all about love.
That's why the producers keep saying it will be bittersweet. Because they're all going to die, but they're all ultimately going to be together.