I put this theory together from 3 different posts in a different theory. My comments strayed pretty far from that specific theory, but I was on a roll. I figured I would create a new theory - I think I bring up some points that aren't often covered in many theories. Enjoy, and please respond with thoughts!
Part I - Desmond can fix everything, Jack's decent into alcoholism, and Free Will.
You know, all of this could have been avoided if Desmond just married Penny to begin with - this all started with Eloise planting a seed of doubt into Desmond when he went to buy the ring, he was letting other people (pun intended) influence his decision making. She basically told him that he does not have free will and he believed in that. He still had a choice but what good is the choice if you are to believe it doesn't exist?
All the Losties have had free will, its always existed for them - whether or not they chose the path of free will or chose to give in brought them all to where they are now.
Remember when Jack was on the airplane bringing his father back in the pilot episode? I think Jack's greatest fear was that he would one day be like his father, and the best symbol for that was the alcoholism. Of course this wasn't his first drink ever, When Jack was drinking his vodka drink on the plane is when the plane hit the turbulence and started crashing. The first thing Jack did when he woke up on the Island was pulling the vodka bottles out of his pocket.
I actually think this whole show is really Jack's decent into alcoholism, becoming LOST as a person, not accepting the fact that he has a choice to be different from his father, he is not fated to follow the same path. Really each of the characters are there for similar reasons, but since Jack is the protagonist, I am focusing on him. I if they land in LAX we will see that similar things that happened to them on the Island will happen back home - the Island is more a metaphor for their self isolation then a physical location, therefore their problems will still persist.
There is a saying "No man is an Island" which means no person can exist in isolation, everyone needs someone.
Charlie seemed to be the only real person that has benefited from the Island - he kicked his drug habit, he found love with Claire and helped take care of Aaron, he sacrificed himself to help save others, knowing the whole time it would result in his death. That one kind of throws me for a loop - I'm not sure how to read into that.
Part II - Why some of the Losties went back to 1977.
To clarify my above post about Jack - I think what is happening on the show is symbolic of Jack's isolation and his fight to free himself of ending up like his father - drunk and alone. Maybe the reason they go back to 1977 is that was right around when Jack was about 10 years old and he got into that fight as a kid to help his friend. The bullies told Jack to stay down, but Jack got up anyway knowing he was probably going to get his butt kicked. But that is when Jack decided he needed to save people and prove to his father he "has what it takes".
Jack made a similar decision in 1977 on the Island - he made his choice then on the Island too. The same thing could probably be said for Sawyer and Kate - Sawyer was about 9 years old when Jacob approached him. Sawyer said he was 36 years old when Ben "put the pacemaker" into Sawyer's heart. That was in 2004. 2004 - 36 = 1968 when Sawyer was born. So it would make sense that it could have very well been 1977 when Sawyer made up his mind to seek out the real Sawyer.
So maybe Jack and Sawyer (possibly others Losties too, but I don't want to make this too long and write about them) will die in 1977. This is because this is when they made their mind up about their life- the created their own fate, essentially dying.
Maybe in an alternate time line, because (or maybe not because) of their actions as adults in 1977, they will be able to figure things out and utilize their own free will to change, thus saving themselves.
I'm sure knowing LOST it will be more complicated then that, but every story has elements of symbolism and metaphorical references, and that is what I look for in good stories.
Part III - John Locke - He was special when he believed it.
What I think is more important that who was actually John's father is the fact that while on the Island, John was powerful, John was whole, John was the hunter he always wanted to be, John was what John chose himself to be the moment he woke up on the beach.
It was only his self doubt and the fact that he felt he had to turn to anyone else to be told what to do that caused his downfall. John allowed himself to be a puppet, he denied his own free will even though it it right in front of him the whole time that he could be what he wanted to be.
John didn't need to follow anyone else, John would have been the leader of the Island if he able to see it, if he had faith in himself. Bad things started happening when John allowed himself to be manipulated by the Others and the Island.
John was special, but because he didn't believe it he allowed himself to be killed.
Remember all the times John lost the use of his legs? It was during periods of self-doubt. When he was laying in the pit o' Dharma bodies he couldn't move his legs, but once he was motivated to get "back to work" he was walking around just fine and he even had a bullet wound through his torso that didn't even bother him.
I don't know what the resolution will be in all this - I do believe John Locke will still prove to be important, or maybe it is just too late for him after all. Maybe the Island provided John with what he wanted in an attempt to manipulate him.
Part IV - Free Will and Suffering
How can anyone really be certain they are making decisions based on their own free will and not based on levels of manipulation in which they are not aware of? If you make a decision to walk across the street, you are only making that decision because someone put a street there at some point, and there is something you desire on the other side.
That reminds me of the whole "To desire to suffer, without desire there is no suffering." I believe that is a Bhuddist quote.
Maybe that is why LOST just gets weirder and weirder, because the characters continue to suffer more and are perpetually getting more LOST - they are losing the time they have left in their lives. The characters will never achieve what they desire because I think most of them don't even know what it is.