Some controversial opinions coming, don't shoot me fellow frog mains...
Greninja doesn't need perfect pivots. The importance of them is often exaggerated by Greninja mains who, IMO, want to make the character seem more complex than he is. The biggest use for perfect pivots is comboing Dtilt into perfect pivot Utilt, and retreating Dtilt is useful, but they aren't a requirement to play the character.
I... don't think Greninja is a particularly difficult character to use.
He has a simple neutral revolving around a very good projectile, fairly safe pokes after the shield nerf, top 3 mobility and probably the second best dashgrab in the game. What he wants to do is fairly simple. Some of his hitboxes do require a lot of precision, but so do ZSS'. Hell, so do Marth's. It's a common trait in this game to have fairly precise hitboxes. Sure, most aren't as precise as a 2-frame active 16f Fair, but 14% and kill potential on an aerial that can be comboed into and only has 18f landing lag has to be balanced somehow. Greninja was hard after his initial nerfs, but he's received a lot of love since then. With good shurikens comes a good character.
Greninja's neutral is underrated overall. It's very hard to crack an evasive Greninja open and apart from Sheik and Sonic, I can't think of a character who he really struggles to win the neutral against. Fox and Pika are tricky but very beatable in neutral. He's got a good shot vs all the other high tiers and starts running rings around the slower low tiers.
It is indeed concerning that Greninja gets left off a high damage combo list. His basic BnB (Nair Usmash) does 30%. Anything that combos into Fair does 20%+. He gets footstool combos at 0 for a guaranteed 44% or a trickier 68%. He has high damage combos off a lot of attacks. I'd say he has combo potential at least as good as Mewtwo's and is only truly outclassed in versatility by autocomboers like Mario, Pika, Sheik and ZSS. His low risk BnBs often do more than theirs though, especially Sheik who loses a lot of combo potential after mid percent while Greninja still gets 20%+ off simple combos into Fair.
IMO Greninja is harder than your average top tier but not so difficult that he should be turning people off. It's not hard to play his neutral, and he has a combination of strengths in safety, camping and combo potential that few other characters have. But maybe I'm just used to him, because I do see other players use him and do terribly and stick him low on their tier lists.