Some additions to your post
Biggumsboi.
-Why not remove the the BOS completely? Make them the National Lawful Guard or something, remnants of the pre war military and police that try hold up order (but aren't exactly doing a good job anymore).
-Remove most other Fallout 1 and 2 West Coast references such as Harold who really deserved better.
-The Super Mutants? Why not make them those twisted human mutants from some of the earlier Fallout 1 advertisement pieces;
https://external-preview.redd.it/Dm...bp&s=6e7c57e1b00d61f53bf74ff8954a1e66e4510245
Call them the Wretched or something. Healthier than Ghouls but in general having lost a lot of their humanity and having form a Cult that hates all normals. (they are just good for use as slaves and "other" purposes)
-Set the game once again twenty-five years after the War
-Get rid of the stupid humor. If you can't do jokes well, don't do them at all.
-Get rid of the radio guy or replace him with a character that makes sense
-Definitely get rid of the "50s but in the future!" mindset. Fallout wasn't "Leave it to Beaver" and "Father knows Best" in a post apocalyptic wasteland with mutants, robots, and energy weapons. (Fallout is what people in the 50s imagined what the future could be; a future civilization and the horror of a nuclear holocaust )
Definitely make the player character separate from James and his forced morality and pathetic outrage when you decide to nuke a town (also something that should be drastically changed) and treats you as if you have just stolen a pie from Mrs Wilson the next door neighbor.