For me, the ending showed us that the ALT timeline was a long con gone bad on the part of the writers. They were shooting for a "keysor soze" or "sixth sense" moment to leave us all in shock over the big reveal, that the ALT timeline is not what we expected at all. Problem is the big reveal fell flat, and cheapened the mythology of LOST (give me a chance...please keep reading).
They roped us in with the opening scene of the season in which the plane never crashes, and the island is on the bottom of the ocean. We all went bananas asking the most logical questions...Did the bomb really go off? Is that what sunk the island? If not, what did? Are we seeing how our characters will ultimately live out their lives? Is the ALT timeline even reality? In the ultimate game of cat and mouse the writers drew us in and kept us guessing, and in an ironic twist we come to find out that the ALT timeline turns out to be a purgatory of sorts, which is what some were theorizing that the island itself was all along. It's almost as if it was a subtle joke by the writers to remind viewers that they were always one step ahead of us.
I understand the ALT timeline. I do...I get it. They're actually dead, all of them dying at different times, some sooner and some later, and now they've reunited in a place they collectively created, which transcends time, to live out some sort of afterlife together. But before the big reveal scene with Jack and his Father, i'm guessing that 95% of us were expecting the ALT to be the ultimate outcome of the events in the island timeline where everyone lives happily ever after. I guess it was in a sense...but not entirely.
The ALT timeline was something no one really expected. My point is that the reason no one expected this ending is because IT DOESN'T MAKE SENSE. I believe that the writers created it primarily as a tool to keep us off their scent, screw with our minds, throw strange new scenarios at us, and blatantly make stuff up. It was a long con gone bad.
Finally, the genius of the show up to this point is that it has refused to let us stick it into any one religious mold, and that there was room for all major religions to read their beliefs into it. We never really did get ultimate answers about the origin of the island, and I think that's fine, because in the final analysis the show was ultimately about the characters. But by creating a scenario in which they actually crafted an afterlife, they undid all of that religious tension and mystery that drew so many into the show in the first place. I got an answer to a question that I never really asked of this show - "What happens when we die?" And to be honest, I think the answer they gave was stupid.