Mostly, the Japanese lost the pilots - who were irreplaceable.
Yes. Even the Japanese recognized this later on...one Japanese admiral (I want to say either Kurita or Ugaki) likened the aerial disaster of Saipan—which went down in American history as the Great Marianas Turkey Shoot—to throwing eggs against a stone wall.
The Imperial Japanese Navy believed in washing out 90% of pilot trainees. All well and good for a short war, but murder in a long war. Paired with the callous lack of concern for pilot safety in aircraft design, the results were disaster.