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I still am kind of confused why some people were in the church and why some were left out. The biggest mystery for me is why Aaron was still a baby in the church scene despite him actually growing up at least a few years in the Original Timeline. Although there could be a number of reasons to justify explaining it I am trying to come up with a plausible one.
I think the people that were not in the church were not there because they were still getting to the point of "letting go" For instance I don't think Ana Lucia REALLY had a huge impact on anyone or took a lot from the island. Maybe she needs to find someone else in her life and make amends and meet up with them. I think Ben wants to spend time being an actual father in an actual family before he is ready to let go. I also think that is why Faraday didn't go. Eloise realized what kind of "purgatory" they were in and she wanted to spend some time as an actual family before they all let go. Plus Faraday just ran into Charlotte and so perhaps love will continue to bloom there. I also think though that before they move on Faraday will have to learn what Eloise did to him on the island and both of them will have to come to terms with it.
As for Aaron I believe he is the trickiest. I can't decide whether or not that was the actual Aaron or just a figurative Aaron. I think the Aaron in the church was supposed to represent the time that Charlie and Claire raised him. However, it appeared (at least I thought) that when Claire gave birth to Aaron in the FST she kind of reacted like it was the son she raised for many years. (Since in the OT Kate told her she would help her figure out how to raise him) Something about the way she said "Its Aaron, Its Aaron" it was almost as if she was giving birth to a kid she raised for plenty of years and was reminiscent of him as a baby. So I believe that the Aaron in the church was kind of just a symbol for Charlie and Claires love together and that the real Aaron will move on someday with his own family and what not.