I should really check out Fallout: New Vegas
In Fallout 3 you have Little Lamplight and Big Town. These are nothing but tropes pretending to be world building. Little Lamplight is the worst offender, considering how it only makes sense if the war happened a year or less ago and these kids were stranded in a cave when they took shelter from the bombing with their teachers.
The BoS being present in Fo3 could be acceptable, their behavior can't. Knights in shining armor are not what the BoS is but that's what they are presented as. Why? Because Bethesda can't make a game without using black and white morality and an organization of elite warriors to join (The Blades, BoS) to save the world.
Even the GECK was a McGuffin done wrong. It's shown in Fallout 2 that it was a suitcase of seeds to replant and restart civilization, not a magical device that can "create life", which even if it was, using it as a water filter has got to be the dumbest thing ever.
Contrary to most people, I get the idea about that game's plot being entirely surrounding the water purifier. It's a nod to the first game where water plays an important role to hook the player and the factions aren't all "fighting to turn it on", they are fighting for controlling a very important asset that can ensure supremacy over the DC wasteland and beyond.
However, it's still a cookie cutter black and white story with the option of being a dick because "violence is funny haha" and it takes the entire central plot of the game when in the first, it was but the first hook into something far more serious.
It violates the idea of what the GECK is, it paints the BoS and the Enclave in a completely wrong way and it doesn't even make sense, considering Megaton's water purifier or even Harold.
Fallout 4 is even worse, the Institute alone takes the fucking cake here.