After reading Shattered Sword it's pretty clear the Japanese were beaten the moment they left port, they did not train to loose, they trained to win to the point the practice scenario's the pilots were taught heavily favored them so the training wasn't realistic, the CAP procedures/doctrine was based around the A6M's lack of 20mm ammunition which meant the decks were kept clear for them to rearm instead of launching bombers, the fire control damage control was centrally organised with a clear pecking order of who was in charge, when those central people were killed no one knew what to do, the ships themselves were poorly designed so when they were hit they burned out, the IJN was a strong force on paper but when the shooting started it had a glass jaw.