Having rewatched the season one pilot and all this talk of clues I thought I would share a few ideas. Firstly when Jack wakes up in the jungle, I thought that the eye as it opened was different to jacks. What if it was Jacobs? Darlton have said that we see Jacob in the pilot but they never said how much. They also said we didn’t hear him speak. Then to note that we see Christian Shepherd say to Vincent to go wake Jack up as he has work to do. This was from missing pieces 9. Now running in consecutive order it seems like the eye is jacks as he wakes but the more I watch the show it isn’t. People assumed in s4 e9 when Ben arrived at Nadias funeral that he had come straight from the desert off that horse but why? It’s not like the producers are going to show every step of his way. The flashforwards operate at different times. We see the main points to show the story but they are not necessarily one after the other. The pilot episode shows this as it goes back and forth from when they crashed, were on the plane etc. when Ben asks the year at the hotel it may have been another time jump from the one in the desert.
People have made light about the object that looks like Bens baton on the ground next to Jack when he wakes up. Some think he may be given the baton by ben in the future and this shows his return. I think this is far too obvious and the object while similar isn’t the same. Also if Jack was to return to the exact same point why would he not remember anything? I feel the eye opening is Jacob awakening to the fact that Locke has finally arrived and so Christian sets Vincent in motion to wake Jack as Jack is part of Jacobs plan and as a doctor is important. Also Jack would be needed to help Claire. Locke later makes a point of having looked into the eye of the island and it was beautiful. The island being conscious must have a soul and this is probably what Locke saw.
Think about the eye opening believed to be Jacks but that I think is Jacobs.
As the eye opens it sets off a chain of events.
1. Locke walks again
2. Christian appears
3. Jacks rushes to beach & saves Claire
4. Rose is cured of cancer but doent know yet
5. Smokey arrives and scours the island
6. Smokey kills the pilot as he is not the pilot that was meant to fly.(widmore employee?)
7. All of the oceanic 6 are part of the same group and section of the plane.
Coincidence or the power of Jacob/the island at work to help those that are needed. Later we see Jacobs eye again at the cabin scene as if Jacob again acknowledges Locke by physically appearing if only briefly. Prior to this he is invisible.
Now for an interesting thought. Ben it seems is not as powerful as Locke. He may have believed to have been the chosen one due to both having a mother called Emily, and problems with childbirth. Annie died in childbirth and this upset Ben greatly. We are led to believe that the child died also but what if the child hasn’t and was taken like aaron off island. Think of Thomas Aarons father. Looked like Ben, could be a coincidence but if he was Bens son then think of the possibilities. Thomas born on the island has a son who is also born on the island. It would create a child with a very strong lineage and one that needs protecting hence why Christian says he is where he is meant to be as the island is not safe as Jacob wants it moved. If Claire is dead then aaron has no constant so if the island goes into the past then he would die so he must be kept alive. That is why aaron isn’t meant to be in the cabin and why he is meant to be found by sawyer and take off island by Kate to be raised until they are called back.
This would also mean that Jacks nephew is Bens grandson.
By bringing the family together then having them all on the island would complete this but what would the signifigance be bar fulfilling some prophecy that is probably in the book of laws that Richard Alpert had.
When we were young nobody died
Nobody got Older
the toughest kid in your street
could always be bought over
Bravo 
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