Carrier Division 5, while the newest in the Kido Butai, was also its strongest. They alone had the air assets that equaled or surpassed American carriers of the time in number. They were also the only Japanese carriers afloat that equalled ours in tonnage, and they were capable of operating at higher speeds than Carrier Division 1[AKAGI and the even slower KAGA].
And the failure of Japan to graduate Naval aircrews in adequate numbers to replace those lost will be a problem they never address successfully [along with failing to rotate pilots for instructor duties, much like their German Allies], and one which will lead from Midway to the Great Marianas Turkey Shoot in the blink of an eye.
At this time, they also are not producing enough naval aircraft. This is a result of the change in production from the Kate to the Judy, and as a result no torpedo strike aircraft are being produced. The Japanese flattops at Midway will not have full air complements, in part due to the fact that they just don’t have the planes. And many of the planes they do have are past their useful lives.
The Japanese seriously underestimated the attrition of warfare in trained pilots, trained crews, planes and ships. They entered the war with the best of all of them, but had no plans to replace them.