Honestly, I lost interest when Pip was infiltrating that base for the griffon who's men were blocking their path.
I just don't get the same interest in it everyone else does, and too many things just threw me out of the story and ruined my suspension of disbelief. Pip seems to be a near flawless character who always manages to do the right thing. I cannot stand such characters. Not once in my short time reading it can I remember them do something that can really considered bad.
It doesn't really have the fell of Fallout for me either. Fallout was where things were though, but they could conceivably get better with a little work. Fallout Equestria just shoves me into a world where it's hopeless and bleak, nothing you can do really makes a big difference.
Neither does it have the feel of Equestria, where things are always a bit hectic and messed up, but never actually bad. Thing in Equestria always ended up getting better somehow.
Fallout Equestria to me is really just a failed attempt at making two things fit together that can't normally go together.
Almost as bad as the Conversion Bureau.
...are we even reading the same story?
Lilpip is a drug addict who abandons her friends, betrays others, massacres an entire village of women and children.
She takes lives without remorse, is "not the Element of Honesty", is perfectly willing to torture and inflict pain on others.
She's a monster. She even admits as such. She's not even one of the elements, and when the time comes to restore equestria with "sunshine and rainbows" she gives herself up because she doesn't deserve to live in it.
Equestria is the way it is because of the naivety of the ones who were in power.
Twilight the OCD pony was willing to go to any length to defend Equestria, even creating the Taint, while sacrificing her own Element, inadvertently creating the monsters of Fallout.
Applejack fought for maintaining the usefulness of the common Earth Pony through technology, inadvertently creating the corporate and bureaucratic nightmare that partially lead to Fallout.
Pinkie Pie only wanted everypony to be happy, and gave herself over to drugs in an attempt to stay happy all the time in an increasingly desperate world, opting to monitor EVERYPONY's actions to keep "her" ponies safe and happy but inadvertently creating the police state and drug-ridden world that lead to Fallout.
Rarity only wanted to generously help her friends with her ability to appreciate beauty and immortalize souls, but in "helping" maintain the Image of her friends inadvertently becomes a mistress of Propaganda and introduces the already worsening world to Black Magic.
Rainbow Dash wanted only to be loyal to Equestria, creating a ministry as best she could to arm the pegasi into an elite Enclave, but her inability to organize or actually discern values beyond "awesomeness" lead to indifference and self-centeredness on the part of the ministry she created, and when the bombs started falling they closed up the sky and took away all the sunshine and rainbows from the fillies and colts that should have grown up with them, inadvertently creating an almost unbeatable enemy and the dreary sunless world of Fallout.
Even, or especially, Fluttershy wanted only to make everypony peaceful and to be kind to everypony, but her desperation at trying to bring about peace led her to create the world's most powerful weapon, the megaspell, in the faint and desperate hope that mutually assured destruction could make everypony realize that war's not worth it. This simple, seemingly rational act, perfectly in character for her, directly, if inadvertently, led to Fallout.
Everypony acted exactly as they would have. The descent of Equestria is shocking and sad, but neither as unbelievable nor as illogical as you think in my opinion.