Oh, no! They weren't dead the whole time! It's just that, at the end of season 5, you know how the detonated the bomb? And they thought it would take them back in time to 2004 so the plane would never crash? Well, in season 6, it was split up into two timelines, i guess? One was what would have happened if they never crashed on the island, and one if the bomb didn't work, but took them back to 2007. And somehow (I'm not sure how though) the timelines were linked, like they were happening at the same time and Desmond knew it, because he's "special" and can go back and forth between them. So it was his mission to tell all the characters in 2004 that there was something more than the lives they were living, hence, he took them to the church at the end where they "moved on." So actually, in 2004, they all were really dead, but in 2007 on the island, they were still alive. But it's just like after all of them died they were ready to move on together and they had to move on together because of the relationships they established while they were living on the island. It's like they were always destined to be together, even if the plane never crashed on the island, kind of like the "universe-course-correcting" element they talked about before. I know I probably contradicted myself in this explanation, but it's what me and my Lost-obsessed friends have agreed upon.
I was pretty satisfied with the ending, even though they didn't answer a lot of questions, but I think the whole show was more about the characters and relationships, rather than details about the Dharma Initiative and other stuff. Oh, and I agree with you about season 5. It was not the best and I think the time-traveling element really turned people off. But all in all, I have to say it's the best show I've ever watched!