Armed with the knowledge that we now have, let's try to figure some stuff out.
Egyptian writing is everywhere, even in the cave of light and the stopper. The egyptians believed very heavily in the afterlife and had the capability to build pyramids. It seems likely to me that the island has ALWAYS been present. They came to the island and found the cave of light and made the mistake of tapping into the light, causing need for the stopper. This probably caused the creation of a smoke monster and began the need for someone to guard the light and the island, ultimately ending in the cycle repeating with two more taking the role of the light and the dark just as Jacob and the Man in Black took the role from their "mother".
The mother, I think, was somehow cast in both roles- forced to protect the island yet imbued with the evil power as well. She knew that the island would eventually be prey to those who seek it's power if she left yet I believe she wanted to leave as well. This is why she pushed Jacob and MIB into the roles so that SHE could move on.
The light is life, death, and rebirth. A little bit is inside everyone. Without the light, however, the cycle of life ends and there is no afterlife. That has always been what's at stake- the island is necessary for life to continue and to continue on afterwards. The Light is basically the energy that is a soul.
MIB was lied to and told there was nothing outside the island so that he could be put into the dark role. What I don't entirely get, though, is why he can't leave the island and jacob can. The island is a mystical force, and it is kind of cheap for the writers to leave certain questions as being relegated to "it was the island's wishes" but this is one of those things I think they wanted us to conclude. Perhaps it's that the man in black was a ghost (as smokey of course) and was stuck on the island like Michael and the whisperers. He can't leave because of what he did (killing his mother and then, ya' know, TONS of people). And if he left then the that would unhinge the entire system, allowing the souls of those who died to go free without having to pay for what they did to be trapped there. It would cause evil to have no ethereal ramification.
MIB became capable of being killed after the stopper was released. This leads me to believe that his power is based entirely off the presence of the light. He died and was just plain stark dead. No afterlife, nothing, because the light was at that point gone. I think becoming the island's protector gives you a small bit of the power of the light, and as such you can guide people and grant them gifts of life. It's a counter-balance to having a roaming evil capable of taking different forms. The removal of the stopper and therefore the light was like stripping away the power entirely. Jack's job was to protect the island and that's exactly why he had desmond remove the stopper, to bring things back to zero.
The entire sideways universe I think exists beside the losties, but perhaps it's different to different people. I think others there were given a second chance and could find those who they were connected to in past lives, their constants, and move on, however the losties sideways is different from Joe Shmoes in that Joe Shmoe wouldn't read in the paper about the mysterious disappearance of multiple people in a church. I don't think it was reserved just for those who came to the island. Were it so, that would somewhat cheapen the whole reason for protecting the light- not to protect the afterlife for themselves but for all of humanity. Those who died in the afterlife, perhaps that's their hell. Keamy was evil and therefore has to die again. Anthony Cooper ended up a vegetable. Charles Widmore redeemed himself in the end by coming to the aid of the island and bringing Desmond.
Eloise Hawking (or Widmore) I think has a uniqueness about her in that she seems to be a knowing, guiding force. Juliet said "we can go dutch" before she died, slipping into the afterlife and back for a split second. Perhaps after killing her own son, a part of her, she became capable of seeing through to the other side and knew that things had to happen a certain way. She tried to stop Desmond's intervention because normally people must find each-other by themselves, however Desmond is exactly who brought them all together to begin with by crashing the plane, so it was his role to do so.
I love how Desmond had to push the button to save the world as a modern equivalent of the protector of the island stopping the uncorking of the light since the Swan basically was a modern stopper. When he turned the key, however, I think he became unhinged in that his mind could look into the afterlife. The whole "Flashes Before Your Eyes" episode was probably him looking into the afterlife in which a second chance was possible. Eloise wasn't really Eloise but a construct of the afterlife to guide Desmond. Same in the sideways universe. So maybe the entire time we thought she had some deep insight into the working of the universe, that was just her after she died in which she would understand such things. She never once had a "no, you don't buy the ring" scene in the real world, she just knew about the island.
She stayed behind as well as Daniel and Miles and others because they are still there to guide the rest "home" (into wherever those in the church went, whatever you want to call it). Dan will lead Charlotte there someday, Miles will lead his father, and so on. I think the reason they did that was just for lack of time; the episode was already no-BS no-time-wasted so that would just make it more that would have to be packed in. I think Walt will find his own way someday but his afterlife will be different because he'll still get to live out his whole life and maybe the island won't be the most important place nor the most important relations in his life.
Those who were "Special" I think were those who were imbued with an abundance of light. Walt could make things happen because he had a connection with the source of life. Locke healed so fast because he was connected to the light by having an abundance of it.
I'm still not sure why babies who were conceived on the island can't be born. Ethan WOULD be an exception however Horace and Amy could have easily left the island to conceive. Perhaps being in such close proximity to the light, it overloads the unborn child since, at some point, (probably at the point the deaths occur) the light must enter a living being. That's about as close to a theory as I can get. The statue of Tawaret was probably made by the egyptians hoping for birth to occur there.
Oh yeah, and one more interesting thing to mull over: in the foot statue there's an egyptian-style image of an eye with many hands extending down and touching people. Perhaps this is the only hint we have at those who came before, the beings who imbued life to begin with.
There's so much to think about- I think a lot of what I wrote, though, will be what I consider my answers. It will probably be a while before we get anything definitive.