The only spoilers in this theory are from interviews with the producer that are out there in the public.
I am reading over and over again that alt is the end and finding that I am more and more dissatisfied with this possibility. All the theories revolve around this notion that Jack will do something heroic and sink the island underwater AND move it to some point in the 70's so that the "Alt" reality can show us the effect of this reset. Like many others, I take issue with this primarily because it erases character development. I don't know about you, but I found the Kate/Claire story to be pretty boring and contrived.
I am hopeful that the people in charge of the show feel the same way. I read in an interview that the island underwater is supposed to be a symbol of sorts that resetting time and trying to change the past is a bad thing - that in acting out of selfishness for your own well-being, you cause the destruction of other people's lives. I know they talk a lot, but this ties in nicely with the reoccurring theme of destiny that has been around from the beginning. It also raises an interesting point on free will. It is easy to conclude that by changing the past, you are taking free will into your own hands. But think about it. It's only the free will of a few. For everyone else who is indirectly affected by your actions to change the past, free will is taken out of their hands. Their lives are altered not because they had a choice, but because you wanted to change your own.
This notion immediately discredits the idea that Alt is the end. If Alt is supposed to be an improved universe for the Losties and the direct result of a reset in time made by Jack, it discredits the position that changing the past is wrong. In fact, it sends across the opposite message and implies it's a good thing if we see that they are all better off in this world than they were on the island.
On the contrary, I think we have already been watching the consequences of changing the past all along. I think the past was changed when Jacob, Richard, and other actors of the island came into the Losties lives in the first place. Everything leading up to the plane crash and after has always appeared to be part of some design. You've got Jacob coming in and touching select individuals, lists with Losties' names on them, Daniel's mom making sure he goes back despite knowing what happens (or maybe because of?), Widmore sending Desmond on the race that led him to the island, Christian's body NOT getting lost pre-flight(presuming his body was in fact necessary to get to the island as Eloise indicated) etc. We know Jacob "brings" people to the island, as opposed to inviting them - meaning they don't have a choice in the matter. Jacob, in a sense, has robbed people of their free will by forcing the island upon them. So taking the producer's point about selfishness and chan! ging time, Jacob has been the perpetrator all along - and I suspect we are about to see very ugly events unfold on the island. Ugly things that happen to these people that would not happen if Jacob and the island had never come to them in the first place
So what is the alternate time line if not the end? I think it's time as it was always meant to play out. It's what happened when Kate did get in trouble for stealing the lunch box and when Sawyer couldn't finish his letter to dwell on revenge. It's when Jack is more susceptible to his father's influence because Jacob didn't tell him to give it a push (which could be why he now believes nothing is irreversible - something his father seemed more inclined to believe). Why is the island underwater? No idea! I don't think it was jug head. There are too many variables that make that unrealistic (like the fact that the Losties appear to be on the same island jug head was detonated on and it is not underwater). The producers said it was a mystery and not necessarily jug head. Maybe we'll find it's the reason Jacob went after them in the first place.
I am probably wrong, but what I like about this idea more than Alt is the end is that it answers a lot of questions that would otherwise go unanswered. It answers the mysteries about the lists, about why Jacob brings people, and little things, like Cindy the flight attendant, and Libby showing up in odd places (if we find out she is connected to the island all along), and why the numbers were given to Hurly specifically, etc. If Alt is merely the end and another reset that comes at the end of a war, all these things are immaterial.