I suspect that much the RotNR storyline has been incorporated into Mando S3/Ahsoka/upcoming Filoniverse content, rather than being dropped outright. Given the interconnected nature of the Filoniverse RotNR’s story would probably directly affect the other shows (e.g. Thrawn’s return), necessitating it being retained in some form. And the NR subplots do feel shoehorned in places, especially in Ahsoka.
If you go by that theory, it would seem as though the NR WAS supposed to be incompetent all along. Presumably this is a consequence of the Sequel Trilogy portraying them as such.