Most likely an inflexible approach to training.
The IJN had a super tough program for their naval pilots - and disqualified
a number of candidates on minor issues.
They wanted an elite group and raised the bar considerably.
<<<
officer was charged for an offence - an equipment loss - being drunk on
duty - his record was forever blemished. Even if he performed exceedingly
well in latter years, a top mark could not be put on his record due to the
earlier incident (even if it occurred many years ago). >>>>
But when the combat losses started impacting, the system couldn't cope.
It also didn't help that a irrational mentality/ cult had take over the
military corps during the 1930s - a mentality that placed tremendous faith
on the "Japanese fighting spirit" over all other considerations, including
training and tactics.
Of course, the issue of insufficent fuel and production played a great part
in the equation too.