But can you really single Nagumo out as in my opinion the IJN was a giant waste of metal, it was poorly used and badly led right from the start.
After Pearl Harbor which as you have indicated was mismanaged the Japanese surface fleet just seemed to sail from one disaster to the next.
They did sail from one disaster to another but, with optimism each time that they would win, this time.
Back when the Japanese Navy started to become modern (late 1800s), they modeled the culture of their navy after the Royal Navy. The RN viewed intelligence as "un-gentlemanly!" The signals being sent should be as private as a gentleman receiving mail. A gentleman does not read any other's mail. While other navies started using signal intelligence in the early 1900s, the IJN looked upon this as being beneath them. So at the start of WW-2, they were so far behind in naval intelligence they were not really in the game!
The war in the Pacific was also as 'racial' as it was nationalistic! The US shared with its Allies that it had broken the Japanese naval code. Late in 1943, a German spy in the USSR passed the word to Berlin, which passed it to Tokyo. The Japanese did not believe because, it is so hard for an Occidental to understand regular Japanese, how are they going to understand Japanese that is coded? (Simple, team cryptographer with a translator! No one suspected that the US Navy not being surprised at Midway Island or Adm. Yamamoto being shot down four hundred miles behind from lines as a leak in intelligence?)
The other factor that doomed the IJN promotions during peacetime, often does not place the best warrior leaders in command of combat commands. So, people like Nagumo were symptom of the problem, not just the problem. Without good intelligence leaders make one mistake after another. Nagumo did not believe in carrier warfare, so he often disgard good decisions by competent subordinates because they were pro-carrier warfare and he was still believed in pro-battleship warfare. (Advice such as taking six fleet carriers to Midway in the carrier strike group instead of four.)
Now, even if better leadership existed within the IJN, it was only a matter of time before America's production would over power the Japanese. America beat Japan with only 20% of its production. Europe was America's first priority and 80% of the war production headed across the Atlantic Ocean!