The ALT is Free Will by GribFritz

This isn't a complete theory on the end of the show or anything like that. It's simply a theory on what the ALT is. I'm theorizing at what the ALT is or represents, not why it exists (unfortunately, I wish I knew that one).

The ALT is Free Will. This means that our regular timeline is Fate/Destiny. I believe this is why characters are able to possibly learn from their mistakes in the ALT and take different actions due to free will. Just think of the countless times the Losties just did NOT learn their lesson. Sayid, I will torture, I won't torture, for example. The character's seem very reluctant to change their tunes over the course of the first several seasons. Wasn't anyone else screaming at their TV "you just said you would never torture again like 3 weeks ago!"

They're here for a reason. It's their destiny. Why is it their destiny? Because in the ALT, their free will has created similar situations. In the ALT, Ben had to choose between Alex and Power. So in our timeline, he is destined to choose between Alex and Power (notice how ALT happened first). In the ALT, Jack saves Charlie's life (suffocation). So in our timeline, Jack is destined to save Charlie's life (strangulation, also notice how ALT happened first). Ethan tends to Claire as she gets close to delivery in the ALT. So in our timeline, Ethan is destined to tend to Claire as she gets close to deliver (again, ALT happens first). I also found it amusing that in the ALT, Kate bangs the marshall's head on the sink, while on the plane he was hit in the head by a suitcase. Unfortunately, ALT happens last here, but I still like the example. Now if only we discover the marshall dies a few days later, that would help, which leads us to...

The other major part of my theory is course-correction. Why did Charlie have to die? Why did his course need to be corrected? I believe in the ALT, Charlie will die. When he dies in the ALT, that is the signal for it to be his destiny to die in our timeline. This is why he MUST die and will be course-corrected until it happens. Whatever happened, happened. Actually, whatever happened in our timeline, happened in the ALT. Well, not EVERYTHING, but major events. If not Charlie, the fact could be illustrated with Arzt blowing up in a Chem lab. If he dies in the ALT, he must die in the regular timeline. I really want to see that.

Roger and Ben still went to the island in the ALT. There was no mention of Ben's mother ("I wanted so much more for you", not "your mother and I wanted so much more for you," for example). I believe we can assume she died. I'm guessing she died in the ALT just after giving birth, which means she had to die in our timeline after giving birth to Ben.

These are just some examples I thought up. I'm sure people can think of examples from the show that refute the theory, but I think it's a decent theory ;-)

As a final thought, perhaps the lighthouse looks into the ALT, and not into the past of our timeline. It may explain how Jacob knows who to pick for candidates. He sees our Losties, exercising free will, so he knows how they will act and react. He then gives them that little push (hypocrite much?) toward the island. Seeing what they've achieved with free will in the ALT gives Jacob an edge in the game, as he knows what their Destinies will be in our timeline. As our Losties fail in some way in the ALT, Jacob crosses them off until only the perfect candidate remains.