Actually, Fallout:Equestria did preseve most of the "War is Hell" tone, in fact, I would say that it even expanded it. I'm not trying to belittle Fallout with that, it's great at what it is, being an atmospheric game, but the fanfiction's literary medium was inevitably more appropriate for long discussions about ambigous morality, idealism, cynicism, struggles for survival, and the fall of civilization, the nature of tyrannies, not to mention the protagonist's characterization, struggling to find good in herself wheh there is almost nothing good remaining in the world.
Besides, the 50's retro theme itself was used as an intentionally dissonant element in the original Fallout, it's whole point was being a painfully naive andsimplicistic past, so the pony theme kinda replaces that. It has the same effect, with the flasbacks to the pre-war era ponies, with the posters, in-jokes, locations, bringing up the same feeling that "God, how could something so innocent and idealistic go so horribly wrong?"