First off, thank you Trifroze for responding with a good post and not memeing me.
Dthrow sets up for fair if they DI in. It doesn't combo, but since its a huge sword, things are different. So, greninja can cover every option IME. Jump away isn't safe since ninja is faster in the air than almost anyone and can fair you, and you do NOT want to get fair'd while jumping towards the blastzone. Then there is B-throw, which does 8% and if they are DIing away for Dthrow will make them DI in, which puts them in a ****ty spot where you can u-smash a landing option or f-smash an airdodge attempted landing.
I'd argue his smashes are overall solid, considering their disjoint on such a mobile character.
The main thing they do is provide all kinds of psuedo 50/50 kill setups. Say you are landing at 100%, are there any options which win against usmash AND fsmash? Throw in utilt to also kill confirm (DI behind is the only way to survive, but then he gets bair which can kill later anyways) and I'd say no one is truly safe, even if they know the MU.
Another example, and something you touched on, is nair. If you get nair'd and greninja has enough stage, you are in another guessing game. Yes, DI away + airdodge beats Usmash (not at all percentages, but it narrows it greatly)... but if the greninja is jump canceling his usmash (and he should) you have to airdodge preemptively. This dies to walk forward F-smash.
The fact usmash exists makes f-smash stronger, since they have to dodge early to avoid the setup hit and f-smash loves that. Fsmash also often gets really early kills if someone does know the MU, because they are going to be DIing away to not get kill confirmed by dtilt.
In general, I think all his setups have *but if you choose this option, you can kill them for counterplay* so I don't think his kill potential drops dramatically if you know the MU. Usmash in general can cover lots of ****, since you can charge it to force airdodge then the 'sour' hit can send them offstage pretty harshly... again, DI away on landing is something that saves you from dtilt but in all other occasions kills you sooner.
Ftilt is now 'safeish' with 20 recovery frames.
But, rather than tilts, he often uses his great jabs. They have good range, make his aerials supremely safe on shield, and, very importantly, BOTH jab 1 and 2 have a FAF of 22. This means he gets more layers of yomi when he hits you, because he can choose all kinds of jab options. These are extremely useful, and work at a range where other characters are using their safe tilts.
Dsmash is admittedly meh, but its nice to have a roll coverage option.
If you learn his footstools (confirmed from nair btw, which is big. Other characters can do work from footstools but have to land one in neutral which is basically impossible if the opponent is knowledgeable) his damage output is pretty insane. I'm not great, but I can land nair (11) footstool dair (8) nair (soft 6, hard 11), then their percentage determines the followup but often gives you a guaranteed grab, or even a fsmash at lower percentages. This is another trap, because immediate airdodge loses to charge smash and jump away sets up the usmash stuff that we all know, or fair kills.
Not having an aerial he can swing at an airdodge and then followup on is a problem, but he plays this differently. He forces an airdodge, then fastfalls thru you with uair, bringing you down (with linking, barely DIable hits) into utilt or usmash kill confirms. If he suspects your DI, he can turn around on landing and utilt, giving you DI forwards instead of backwards and killing you with uair. Uair itself works as the trap, because you either airdodge the ascending greninja or you don't, you can react to his jump being a full or short hop, and if he does it correctly you have landing -> usmash to also work with.
Yea, his OOS is meh, buts its gotten better to not be a true weakness and he still has f3 jab... ehhh, he shouldn't be shielding as much as others and this is a true weakness.
But I feel he kills with such adjustable options that even if you know the MU, you are in trouble if he is landing his setups. I can see people learning to avoid the falling aerials A-la ZSS, but in many MUs even a powershielded fair is safe, and nair/crossup nair / jabs are so good... Relying on outboxing him is a threat vs fsmash in any situation, and looooots of dodge situations get destroyed by Shadow Sneak.
I just can't think of a safe way to avoid his kill setups, and I think about him a lot. Just always hold away? Even then, he has options.
Additionally, if you opt to go to the ledge, the mixup between dropzone bair and hydro pump is deadly. Lots of characters are totally screwed if they get hit by fair far enough out, because if they can barely make the ledge timing a hydro pump is totally in your hands and leads to guaranteed charged dsmash.. which, past like 100%, will either kill or reset the situation cross stage.
And since I learned perfect pivoting as soon as it was available and have it pretty committed to muscle memory, he actually has some of the most mobile dtilt and utilts. Characters with bad air accel really REALLY struggle to land vs utilt.
PP away dtilt and PP away jab are very very solid boxing options, I'd say his ground/frame game isn't bad at all with this in context.
Regardless, thank you for the discussion. When you play greninja and someone escapes your kill options, you feel like you could have done something else and killed them. Maybe that feeling is wrong, but I don't think so.
Thank you for giving a real reason. I'd add that a lot of those problems you listed apply to ZSS, but do you feel she makes up for it with better disadvantage? Because thats the one I cannot deny, his disadvantage isn't great. f8 counter, fast jabs, shadow sneak, and great mobility make it manageable, as well as a strong neutral and a kit that grows extremely terrifying with rage. Correct rage, you get uthrow uair kill confirms, as well as utilt uair killing earlier and earlier.
And once the uair doesn't combo from utilt, shadow sneak kills you for airdodgeing, as does uair spike.
Ok ill stop now.