First things first - ZSS' jab does not combo into Up B against us even at 999%, we can shield long before it would combo. A frame perfect Utilt is harder to test but it doesn't look like that combos either.
Now, I've labbed a few scenarios and ideas Re. Marth.
First off I should mention that Greninja should never just be sitting in shield waiting to punish Marth, making himself free to Marth's spacing. He should never be sitting in shield ever. His OoS game is garbage, we know this. It's his other strengths that offset it (his OoS game is his last big weakness, too). I feel like this whole discussion has kind of ignored Greninja's superior mobility and ability to get in on Marth by using his speed, running into shield to get hit with a non-tipper that he CAN punish, simply darting around outside Marth's range, etc.
The moves Greninja has to hit his "blind spot" are up angled Ftilt (best/safest option), Bair (fine), Nair (fine), Fsmash (good when it hits but requires them to fall a bit low), dash forward sweetspot Usmash (slowish, but works), sourspot Usmash (slowish, but works) and Fair (slow). There's also perfect pivot Utilt which is good but hard to execute and then crap like Shadow Sneak and Dair that you shouldn't be using. In short, I understand that random SHADs in neutral aren't what make Marth good against him, but I wanted to make it clear that they are not free. You cannot just spam SHAD to approach Greninja.
Greninja slightly outranges Marth's Fair with his own Fair, Ftilt and Fsmash.
Marth's jab is good against us because our fall speed forces us to land when hit by it until really high percents, basically giving him free grabs at certain percents. Marth's jab can also true combo into tipper Utilt against us pretty reliably at kill percent, though it does NOT true combo into Fsmash (we can shield until we can double jump airdodge away) and I couldn't get it to true combo into Ftilt or Dtilt. Tipper jab can combo into itself (not for long though) and Utilt.
We can, however, Shadow Sneak out of Marth's jab's hitstun until it starts to put us in tumble hitstun, which doesn't happen until really high percents. So at kill percent, we can SS out of the jab and punish Marth if he actually goes for another attack. Marth has time to shield though, so it's a mixup, but it can still be pretty scary.
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SHAD as a reactive punish to shuriken. Let's say you react perfectly to shuriken's startup and start SHADing on frame 13 after a 12 frame reaction time. That won't happen due to controller lag, normal human reaction time being more than 12 frames and the fact that you simply aren't going to react to frame 1 of shuriken's animation, but whatever. So frame 13 is the input frame, and on frame 14 you begin your SHAD towards Greninja, which takes 37 frames to fully execute (5 frame jumpsquat, 32 frame airdodge). The SHAD ended on frame 50. It's now frame 51. Greninja finished his shuriken on frame 45 and already buffered an up angled Ftilt which will hit on frame 55.
Marth could buffer an Uair which starts on frame 51 and comes out on frame 55, so this will trade with Ftilt. To actually hit with the Uair, Marth would have to jump into Greninja. I don't know the exact frame data behind Marth's aerial inertia and deceleration, so I don't know whether he would be able to pull back after baiting our reaction, but I would imagine we could react to Marth drifting towards us in time and throw up our shield instead of Ftilt. If Marth crashes into our shield with any aerial buffered from a SHAD including Uair we get a free punish (jab I know works, grab and Dtilt probably do).
Marth could use Fair or Nair, but neither will come out until frame 56 and he will get hit with Ftilt if he doesn't pull back properly.
Remember if Marth tries to stay in the range where a perfectly spaced Fair or Nair will hit Greninja, Ftilt will catch him because it comes out slightly faster. So on reaction to Marth SHADing in, Greninja is better off using up angled Ftilt than shielding.
If Marth pulls back really early, he can hit Greninja's extended hurtbox with his disjointed Fair and be safe. But in this case, if Greninja doesn't use Ftilt (again I'm not sure if Greninja can react to the inertia to know what to do but it seems like he could) Marth just Fair'd nothing and will eat a guaranteed dash grab.
So my point is, Marth SHADing in on reaction to a shuriken toss does not result in any sort of guaranteed punish, it's actually quite a complex situation where either character could come out on top. Greninja is not shut down completely because his Ftilt both outranges Marth's Fair and will beat it out in a perfect reactionary scenario where Marth is still in the range where Fair could hit Greninja or his shield.
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Regarding full hop retreating Fair. You have to be extremely close to actually hit our shield with a tippered full hop retreating Fair. As in, you have to be standing in or dash well inside our jab range. Not the safest thing to set up.
If you whiff slightly, we get a guaranteed full hop Fair OoS punish no matter how much you pull back.
If you hit with a non-tipper, we get a guaranteed full hop Fair OoS punish no matter how much you pull back.
If you tipper our shield you are safe from a guaranteed punish. However, it seems like Marth would be safe from pretty much every character in this situation? Unless I'm missing something/have misunderstood you completely?
Anyway, Greninja drops shield and dashes toward Marth. Marth can landing Fair while still retreating, but if Greninja keeps dashing he will go behind Marth and can pivot grab or Fsmash. Greninja could shield, and punish the Fair if it's inside tipper range. Marth could choose to not Fair and instead tomahawk grab our shield. Or Greninja could avoid the situation completely by using RAR rising full hop Bair against Marth as he was running toward him. You could also Fair, but it's a bit slower. Effectively because Greninja's dash speed is so fast, Marth doesn't get free spacing out of this scenario.
Incidentally, Mac also has a very fast dash speed and could probably use that to get close to Marth after this scenario. However he doesn't have the Fair punish or RAR Bair option that Greninja has.
If I have misunderstood you please let me know but I don't think this scenario costs us the MU or anything because we have decent options against it.
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Retreating SH Fair, landing or not, is safe on our shield if tippered. But again I must go back to, surely it's safe against every character? Greninja has a top 6 dash speed and a top 5 dash grab, if he can't get a guaranteed punish I don't think many cahracters could.
Overall, I feel like a lot of Marth's safety against Greninja can be applied to all but a select few MUs like Sonic and maybe Sheik and ZSS due to their down Bs. But this safety doesn't cost us the MU, it's something that a lot of characters have to deal with. Marth SHADing into our blind spot isn't a huge deal either, as we do have options to cover it and some of our options can actually outrange Marth.
I hope you found this analysis insightful?