Many questions have arisen about ALT, specifically why is the island underwater? what happened to dharma? why is Ben in ALT if he was on the island that sunk? These are all good questions, but really unnecessary to understand ALT.
The ALT timeline is one of a few things: this timeline takes place after Jacob's death...not a result of anything (i.e. jughead). ALT is simply the next iteration of the loop. But this iteration of the loop is special. Why is it special? Because it's different. Why is it different? Simple, Jacob was murdered.
We've been shown a very special scene in LA X that shows us something about our on-island duo. In LA X, Jacob approaches Hurley in the forest while Sayid laid dying. Jacob tells Hurley to take him to the Temple where he can be healed. Hurley agrees. An interesting part of that scene is that Jacob never touched anything. Not Hurley, not dying Sayid. Why didn't he just lay his hand on Sayid like he did with Locke, after his 10 story drop, and bring him back? He couldn't because Jacob is dead. More on this later.
As many many people have theorized, Jacob died willingly...as if he planned on it. ALT is Jacob's plan....the next step to his endgame.
Let's shoot ahead to the point in the island's timeline where the loops restarts (not sure when this is). When the loop restarts for it's 10th millionth time, it's different because Jacob exists differently. He exists more in the spiritual sense. But remember, he can't touch anybody, therefore he can't "push" anybody toward the island.
If Jacob never touched the losties:
Note: when I talk about change, it's personal change...specifically personality/beliefs.
SAWYER
Sawyer doesn't get a pen...doesn't become a conman, becomes a forgiving person. This happens at childhood so his change is more drastic. Sawyers 'path' is changed at this point.
SUN & JIN
Doesn't get the marriage words of advice...they become more and more apart/takes each other for granted. Their 'path' is changed at this point.
KATE
Continues to steal...but is innocent as she stated. Sill on the run, but for a different reason.
SAYID
Walks across the street together with Nadia. And they both live...or Sayid dies by pushing Nadia out of the way and Sayid's conscience jumps to dead Sayid on island. I'm unclear wether Sayid is still a torturer or not.
DESMOND
Doesn't throw the ring into the river...Decides to propose to Penny
And the most important three:
HURLEY
His change is different. He was really never pushed to do anything. Jacob only gave him the guitar case. But Hurley has good luck now.
JACK
When Jacob gave him a candy bar, he gave him a candy bar, nothing more. He wanted to meet Jack, well...because he's special. Jack is still the same Jack. Still a doctor. Still tries to fix everything. But, something else is pushing Jack. Someone stopped Christian's coffin from making on the plane. This happened because someone wants Jack to meet Locke in the lost luggage office. More on this later.
LOCKE
You would think Locke doesn't get healed after his fall because Jacob can't touch him. One may ask, "then how could he come back to life?"
This answer is the simplest of the bunch, Locke was NEVER healed by Jacob. He was simply there for when he awoke after his fall. You could say the island healed him, or even destiny healed him, or he just got the wind knocked out of him...but not Jacob. Jacob is just a man, much like MiB keeps saying about himself. Just think, if Jacob really brought John back to life, why wouldn't he have just healed his spine at the same time? Jacob isn't a god, demigod, deity, and thank god not those damn nanobots. We where simply lead to believe he was some type of God. When you juxtapose the scene in LA X which the "touch" scenes; we are shown one thing. Jacob's 'Touch' means one thing, he was alive at that point in time. And now he is dead. Because Jacob's touch is really a push.
If Jacob is just human, how can he appear to people while being dead? I'll answer the question with another question...how can Charlie appear to Hurley? MiB was never posing as Charlie. Just like MiB was never posing as Jacob to Hurley. And why MiB wasn't posing as that blonde kid.
Now, since Lost deals with the snowball effect, people affecting other people's lives, affects others, upon others, etc. This is what Jacob's "touch" is. He says what's needed to be said, does what's needed to be done in order to 'push' you in a direction. For example, I say to you, "Man, thats a great shirt." And you were second guessing the shirt this morning. Now you wear that shirt to an interview and get the job. Now, if I had never had said that I liked the shirt, you would have thrown it away and therefore worn a different shirt to the interview and not had gotten the job because you're shirt looked unprofessional. See? There's no black magic here. Jacob mastered this art, it took a few hundred/thousand years to do so.
You can start to understand why Ben was a teacher. And the answer is simple: Ben never went to the island. Neither did Ethan. You need to remember, all the key players were "pushed" to the island. After Ben's mom died on the side of the road giving birth, Horas was never there to help out therefore Roger never joined Dharma. Horas wasn't there because he wasn't in Dharma. He still fathered Ethan but off-island. Thats why Ethan was working at the Hospital and not dead on the submerged island.
Now for the main difference between the timelines. Jacob 'pushed' one timeline. Now that he's dead, someone else is 'pushing' ALT. The missing coffin, the missing box of knives points to this fact.
I've read many comments from people who believe ALT is purposeless and a waste of time. It's actually the opposite. Think back to the conversation on the beach between Jacob and MiB. MiB says, "it always ends the same"...this also can mean "people don't change. they fight, destroy, corrupt, etc." ALT is Jacob's way of proving MiB wrong, people do change when left alone with their free will and even free will can change a person. He needed to prove this to MiB first by changing the Losites, by 'pushing' them down their different paths. So MiB could see them for who they're really NOT. Then showing the Losties, untouched/unpushed and their lives are drastically different.
Fin.