I think you answered your own question there, dead. LOL
Only a few of the many people in LOST showed up at the church. I am not sure we shouldn’t infer that some of the others might be in the church but the producers couldn’t work out principal photography contracts in time. Still, as you point out, Faraday isn’t there, nor is his mother, nor Michael, nor Walter, nor any of the others who didn’t click with any of our principals. Lapidus isn’t there and if anybody has developed from the beginning, he did.
So maybe they didn’t quite think things through enough, or, as you say, ran out of episodes and couldn’t be bothered to invite Jeff Fahey for the church shoot (we could safely infer his life in the sideways reality from that event, yes?)
Or perhaps the focus was never to be on those characters who appeared with the freighter. The story belonged to those who were on Oceanic 815. The exceptions were Desmond/Penny and Juliet because they lived with the survivors, interacted, and became part of the group.
Faraday's mother is the real mystery for me. She knew way more than everybody else and nobody ever explained why. And Desmond told her that her son wasn't going with him and the gang, but I still don't get why. Most of the important people were there, except the really bad ones - the irredeemable ones (like Keemey.) Faraday wasn't a bad guy.
Walt just left the island as a kid and forgot about them like it was a bad dream.
I think your’e pretty much on target about why some weren’t in hte church at the end, but as far as Faraday, his mother asks Desmond if he would be “taking” Faraday, to which I believe Desmond says “not at this time” which suggests there is a different “time” for Faraday. But that conflicts with what Christain Shepherd said about the alternate universe/church existing at all times.
Maybe Faraday and his mother, like MIB and his surrogate mother, are special creatures of some sort.