This is always a thing with Bethesda games. Once I get to a certain point, I achieve what is basically demigod status, and I either have to start over from scratch, or, if I want to see the endgame, slog through a bunch of boring, broken feeling stuff that can't touch me.
Since level 50, I've felt like I'm swatting flies, even in survival mode. I'm not actually that good a player, it's just a thing with this style of game. I like to poke around at my own pace, investigate the nooks and crannies, and generally ignore the main story most of the time. But by the time I get around the main story, I can pretty much kill a deathclaw by farting on it.
I should've waited a few months. I have no doubt modders will fix this. Wish I knew how to do it myself, but even if I did, I've barely got time to play the game, let alone mod it.