Hey Nave Ninja, I just finished reading the story so far. It is a very good story, and much better than the canon Fallout 3 plot, specially in somewhat silly parts like The Family's plotline.
Above all, I like how Amata's exit made this story more than simply "Amata goes with the Lone Wanderer, usual Fallout 3 hijinks ensue." No, it was true Alternate Story. The timeline keeps going as normal (including time-travelling tribals acidentaly causing their own existance
), up until Lloyd's leaving the Vault and asking Amata to come with him. Then the Point of Divergence has Amata choosing and accepting Lloyd's offer and coming with him.
THEN even more hijinks ensue. Like:
[spoiler:1cc0858f5b] Burke's survival, The Overseer's attempts to get his daughter back, eventually leading to contact with The Enclave, the larger size of the party, Harkness' and Lucy joining, etc etc...[/spoiler:1cc0858f5b]
I like how what happens has lot of emotional consequences. The trauma following the whole vault escapade, learning the truth about Project Purity, the fateful meeting with Mr. James himself, etc.
Also, another interesting thing you did is also show us Lloyd's glimpse of a parallel timeline in "Who is Lloyd Freeman?"
One thing I notice is that although many bad things have happened because of Amata's decision (Like Burke's survival and Alphonse's attempts to retrieve his daughter), this timeline itself seems better and happier than the canon Fallout 3 timeline, where the Lone Wanderer had at best one companion, seemed to be a loner wanderer and somewhat of a outcast himself. I can see the Fallout 3 lone wanderer ending up wandering forever, whereas the Vault Dweller and the Chosen One both choose to lead their new communities. Lloyd and Amata seem more like the types to settle down somewhere, marry and probrably have lots of kids, probrably either with the Brotherhood or somewhere near Megaton.[/spoiler]