It's important to consider the title of the series itself: "Lost". It's a long, beautiful journey of individuals who, much like ourselves, have problems, issues, either mentally, physically or even metaphysically "broken" (sometimes all three, for instance John Locke, who can never get over his father, is constricted to a wheelchair, and feels he has no overall purpose). Enter the island. A special place, although a place with many unanswered questions (don't expect to ever find out what the light really is etc.), the island gives people a purpose, allowing them to transcend their "broken" lives and "move on". Take John Locke - he is allowed to get over his father, he is allowed to walk again, and he is allowed to find his purpose. Yes he eventually dies - but ends up in a sort of afterlife where he's a "fixed" person, his experiences on the island and in his life allowing him to let go (Desmond's words - "I'm helping him let go" - take on a whole new meaning).
So enter my overarching interpretation of the show: the five planes of reality:
1) The "real" world. This is where the characters originated from, the place the flashbacks and flashforwards were set in. This is where people either live their lives happily (meaning Jacob would never require them) - I think that's why Walt never needed to return to the island and wasn't in the church - when he dies, he goes straight to the fifth plane of reality (remember Locke off the island saying to Abaddon that he doesn't need to come back, seeing that he's been through a lot and ultimately is now a happy teenager, not "broken" at all), or lead unhappy lives, the "broken" people, e.g. Desmond, Oceanic 815, the Others, who Jacob brings to the island (or the people who just ended up there pre-Jacob, like the hunters in Across the Sea or Claudia's People).
2) The island world. Okay, this is technically in the "real" word, but the rules don't apply here. The island is like a bubble (a bloody snowglobe!) with magical properties, due to a light/special energy and water that is essentially the lifeblood of the island, as well as the whole world and its inhabitants, representing, in the words of Jacob and MIB's mother, "life, death, rebirth". This special light/water branches under the whole island, bubbling up in places e.g. the pool in the Temple or the area of the frozen donkey wheel, where the MIB said he harnessed the "water and light" to create a mechanism to transport people off the island. The island, due to its special properties (it really is a sort of "magic box", to use Ben's analogy), can allow people to move on, to let go, while also serving a dual purpose of having some people essentially protect the whole world by looking after the Source and making sure the light doesn't go out.
3) The island as purgatory - Christian Shepherd (now I think this is the REAL Christian Shepherd, as in the one in the flash-sideways/afterlife) told Michael he could "go now" in the freighter before his death. He didn't mean he was allowed to go to the Bright Light (which I talk about later), but that he was allowed to die (which he had been trying to do for a while) and, in order to atone for his sins, act as a whispering, commentating and occasionally intervening spirit on the island along with some others, guiding its current (and I guess it was implied future) inhabitants, e.g. Hurley, along their individual paths. When he's done his duty, I'm sure he'll be able to move on to the final plane of existence.
4) The flash-sideways "waiting room" of the church: the timeless penultimate stage of existence, only reserved for those who still carry some sort of burden after death - in our case, most of our Losties. How is exists is open to interpretation - it may simply be a sort of spiritual waiting room created out of the characters' mutual love for each other, or it could have been created from the detonation of Jughead (although that really may not have even happened) or most likely, Hurley, during his reign as protector as the island, found a way to create it in order to have his friends reunited as last - the whole of Season 6 shows that the characters, before they were reunited and allowed to "leave", had achieved what was burdening them before - Jack's father issues lead him to have a son, Sawyer's morale turmoil lead him to become a cop, etc. - and the final push of remembering their lives and being able to see each other one last time was the final jolt of purpose that allowed them to truly find themselves. Note: this "waiting room" is certainly not heaven - it is simply another reality, represented by the fact all is not happy there either (people still get shot, transgress, Ana Lucia having to wait before remembering, Ben having to wait before being able to move on, etc.) - the point it is a special construct for the main cast of Lost to be able to finally move on, as for them what is really important is each other so it is a chance for them to not only be re-united, but also to be re-united happily, which is why I'm almost 100% sure Hurley created it in a final act of kindness as the leader of the island.
5) The Light. I will not comment on what this is, because it could represent anything - heaven, eden, rebirth, going back to the beginning of a cycle (Buddhist style), or simply yet another plane of existence, but this is where the Losties, once "broken" but now "fixed" by their experiences and ultimate unification, thanks to the "sort of" priest Desmond Hume, are allowed to go. Has nice echoes of the final journey in the boat in Lord of the Rings - you don't know exactly what it is and it's not really heaven, but it's a place for people who have played their part in the cosmic struggle between good and evil, who have found love and a purpose, and "found" themselves, as opposed to being "Lost", are allowed to go. I think the majority of people in the "real" world ultimately go here, but the point is in Lost, our characters had turmoil to sort out, purposes to fufill, islands to protect, so they had a lot of mid-points (the strange "waiting room" church itself) before finally being allowed to "leave", to "move on", words that in the last few episodes have been repeated endlessly.
So there you have it. That, in my opinion, is the ultimate point of Lost.