Honestly, I don't see or hear a lot of criticism for the ninja frog. For starters, you just don't see very many in competitive play and when you do, they typically work their ass off for kills in cool and flashy ways. Greninja doesn't have any "broken" OoS options, superarmor, invincibility frames (beyond his counter, which, duh) and his moveset is pretty balanced overall with strong moves coming out slow and weak moves coming out fast. His skill ceiling (and floor) are fairly high and it takes a fairly high amount of practice and precision to nail his landing Fairs with perfect timing and spacing.
That said, the only criticism I really hear comes from my immediate circle of friends that have been spanked too many times to not throw shade at him. Typical favorites include:
-"Dash attack is broken and shouldn't equal free combos"
-"It's unfair how many recovery options he has" (Hydro pump, Shadow Sneak or Up angled Substitute which can all be used together if needed)
-"Braindead Up Smash for win!"