Most of the lore issues can be explained away in my opinion, doesn't break the game in any way. Super Mutants are known to have multiple origins, meaning multiple factions were working on the FEV. BoS presence can be explained because theres no proof of the faction being huge by that point, so it could have been early predecessors to the modern BoS, which is actually kind of cool, it adds to BoS lore. West Virginia wasn't the only place in the world that didn't get nuked so you've got your facts wrong on that one. West Virginia had low population so if you're trying to confirm a massive casualty loss, then you hit populated areas. So that checks out, and explains why it is so beautiful still.

The thing I do agree with you on are some of the monsters, they went a bit too far in making weird monsters without any real explanation for them (yet) besides "mutations". I'll wait for a mad scientist-esque explanation down the line, hopefully I won't be disappointed.