There were some things the IJN did VERY well. Most notably they practiced extensively for night surface action, and included use of the torpedo in almost all situations.

However there were several things that they did very poorly. The major one is damage control. For instance when not in immediate use USN carriers filled fuel lines on the hanger with CO2, while the IJN did not, meaning at Midway they were all the more likely to burn, which they did. Frankly there are about a half dozen Japanese carriers alone which would likely have been saved had the IJN paid the same attention to damage control training as the USN.

And Japanese radar technology never really took off anywhere near what the US had. By 1944 the effect would be all too clear when at Surigao Strait. When at night 6 US Battleships (of which 5 were rebuilt Pearl Harbor survivors) used radar directed gunnery control to absolutely demolish the IJN force including 2 battleships, showing technology and its proper usage and adoption into doctrine negated Japan's previous forte. Though even well before around Guadalcanal in 1942 the US was able to slowly match Japanese proficiency at night through use of radar and hard knocks.

The concept of overwhelming numbers is also misinformed. It was not really until mid 1943 that the US began to really pull away in numbers, well after the decisive actions of Midway, Coral Sea, and Guadalcanal during all of which the USN was actually severely outnumbered.

The US also had a robust Cryptography program which is how not only were the US and allies were able to get ships into position to stop the advance through the Coral Sea, but come Midway they knew down to the actual day that the Japanese offensive would begin.

I wrote a bit about the Japanese navy's organizational structure here.