"...and from trying to fill every role for all branches of the military"
The F-4 was decent enough at it!

Having superior avionics is never a disadvantage. What you're describing is normal birthing pains for new aircraft. They'll hash whatever bugs are left out before deployment or shortly after, as they arise - powerhouses like the F-22 had to go through similar things and they had a pretty well scoped design to begin with.
Also, the Japanese don't know jack about stealth tech. The J-31 is NOT stealthy.

Hyperbole is correct.