I guess its just a bad writing with plot holes up frontline, no offense to the lead writer Emil Pagliarulo, if only Emil Pagliarulo can understand what make Fallout is Fallout, try to immerse himself into the story he want to tell about, I am sure Fallout 4 could be the best action shooter storytelling open world looting ever made despite a great flaws; voice protagonist and the lack of role-playing mechanic.
to me, Fallout 4 ending is totally rip off from their previous Fallout 3 coolest moments when you choose to blow up the nuke in Megaton? seriously Emil Pagliarulo?!