I'm not saying everyone has to agree with what I am saying here but I feel as though a lot of fans were mad that not everything was answered by the finale, but it was more that the answers weren't give to us in such a direct way as others. So here is how I understood the show...
I figure the best place to start is at The End
WHAT IS THE ALT:
While I think this one was pretty clear I think my interpretation of it is needed for some other questions. The ALT is the middle ground between life and the afterlife where people go in order to find those who were most important during their lives in order to move on to the next step together.
WHY WAS THE ALT AVAILABLE TO THE LOSTIES:
A lot of people on this site seem to be under the interpretation that this availability for the Losties to find each other after death was a special trait given to them for whatever reason, but I saw it as completely different. The ALT is available to EVERYONE, when you die, when I die, when anyone dies the next step is an ALT world where you will find those most important in your life to help you move on. Just as Jack's father had said, "Nobody does it alone," and when he says nobody he means NOBODY and in this ALT everyone has a say in its creation.
WHY DID JACK AND JULIET LEAVE DAVID:
Just as Locke had told Jack after his surgery "You don't have a son Jack." The fact is that David wasn't real. He was just a part of the made up world that Jack and Juliette created for their own reasons. Jack's father issues in his real life had such an impact on him that he created a son for himself to have the bond he never really had. This is why is "son" forgives him and seems to become his pal so fast: because Jack made it that way.
WHY DID ELOISE HAWKING APPEAR TO KNOW EVERYTHING OF THE ALT:
Eloise has already past on, she found those that were most important in her life and moved on with them, but she was still unable to forgive herself for what she did to her son. What better way to find closure with your son then spend time with him in a place where he has created a world that was ideal to him. This is why Eloise does not want Desmond to find out the truth so fast: she fears he will take Daniel with him to move on and she doesn't want him to yet.
WHY DID ELOISE HAWKING APPEAR TO KNOW EVERYTHING IN THE NORMAL TIME LINE:
Simple reason: because she did. She was able to know MOST things because of her son. When Daniel traveled back in time he was trying to figure out how to change things, and while trying to figure this out he took notes on EVERYTHING he experienced. After Eloise killed Daniel his notebook was still left, a book with almost everything that will happen in the future, and she did everything in her power to ensure these events happened.
WHAT CAUSED THE LOSTIES TO FLASH BACK TO 2007:
The same thing that caused the Losties to travel back in time sent them forward to their correct time, a release of the electromagnetic energy from within the island. Juliette was never able to set off the bomb, but during her struggle to do so the drill released the energy causing another flash and the return to 2007.
WHAT HAPPENED TO THE BOMB:
Daniel was right about the bomb being able to negate the energy, but like he always said "whatever happened, happened." So just like every other time the bomb was dropped and the incident occurred. When Radzinsky saw the outcome of the incident he realized he made a mistake. The only way to ensure the energy is not all released is to slowly let some of it out every 108 minuets or detonate the bomb. Although pushing a button every 108 minuets can get annoying, detonating a hydrogen bomb can be worse. This is why the bomb was turned into a last resort: the fail safe key, and just as Daniel had predicted, detonating the bomb negated the energy for good.
WHY COULD WOMEN NOT HAVE BABIES ON THE ISLAND:
As we saw from Desmond going into the electromagnetic energy in the heart of the island, that stuff is not very safe. Through a look at when the last baby was born on island we learn that it was just before the incident occurred: rite before a small amount of electromagnetic energy was being released on the island every 108 minuets. This small amount of energy caused problems during pregnancy, resulting in both the baby and mother's death.
WHY WAS ARRON SPECIAL:
As a mystical person with special powers, he wasn't. As a character who influenced people that resulted in finding their destiny, he was. He was special to Claire in getting her to the island, he was special to Kate to get her to return to the island, but as the psychic had told Claire, he was not special in a supernatural way, the psychic was a fraud who cared only for money not the truth. It was not because of supernatural powers that the others tried to take him, but only because he Juliette wanted a mother who conceived off island to further her research on the inability for women to give birth.