Well, their tactical strategies like mass banzai charges certainly didn’t help matters. They largely abandoned these wasteful tactics by late 1944 and early 1945 and improved their defensive tactics at Iwo Jima and Okinawa but it was by then all for naught.
Japanese merchant ships, vital to the war production, were easy targets for US submarines largely because they used older ships to escort convoys. Conversely Japanese submarines attacked US capital ships instead of going after oilers and replenishment ships.
In addition US Navy fire and damage control was far superior to Japan's navy. US ships stayed afloat to fight again while Japanese ships sank.