What I took away from the final episode is that the whole series has been leading up to Jack having his Bruce Willis moment ala the Sixth Sense. Where he realizes he is dead and can then move on. The island was real just as the producers had promised, as well as the time travel, the Oceanic Six leaving and returning to the island, and the mythology of the island itself. The stuff in the flash sideways this season was ‘real enough’ meaning it didn’t occur while they were living but it was real enough because they collectively created it in order to connect and find one another again in death so that they could all move on.
Jack wasn’t the only one having his Bruce Willis moment of course... they all were.
To really grasp this sort of waypoint you have to discard the concept of time. As Christian pointed out, there isn’t a ‘now’. Time is irrelevant here and to support that I believe that Kate, Lapidus, Miles, Richard, Sawyer, and Claire all lived after Jack’s death. Christian mentions that some of them died before him and some died after. Well the new Oceanic Six... okay ... Ajira Six... lived on and led their lives... we just aren’t privy to what their lives were. On line in particular I feel really supports that idea is Kate’s extremely heartfelt “I missed you” to Jack. It felt as though she had lived on so while Jack had died on the island, she had lived and had time to miss him as the years passed.
So, some may say, well if she lived on, how is she there now in the flash sideways, at the same time as Jack? Again, you have to throw out the concept of time. They are in a place but not a time. Time has no meaning.
If you were to watch the season over and watch just the island portions first and then the flash sideways stuff afterwards (since they essentially took place after Jack’s death which seems contradictory when I just said to throw out the concept of time) then this idea makes a lot more sense.
When Locke insists Jack has no son, he was right. Jack and Juliet’s son only existed in the Flash Sideways so he wasn’t flesh and blood real which is why he wasn’t in the church at the end.
Michael and some of the others weren’t in the church because as Michael said in the church they are trapped on the island for their deeds.
Some of them such as Ana Lucia aren’t ready yet to remember their lives and aren’t ready to move on but they will be at some point.
The island stuff and the Flash Sideways weren’t about two timelines converging, it was that they were all dead and remembering their lives which allowed them to connect to each other and move on. So the Flash Sideways wasn’t really limbo, and it wasn’t purgatory, it was more of a waypoint until they were ready for the next step.