Shaya
Greninja's exceptional tools were all taken out in the first nerf patch lol. Usmash and Hydro Pump were bonkers and both were neutered. He IS a more fleshed out character now with less polarising options but he hasn't received anything that's as "top tier" as those were. His juggling, airdodge traps and edgeguarding WERE exceptional. Now they're just above average.
Shurikens you can argue either way, faster startup is often better than low endlag and aerial shurikens are the best they've ever been (they have prepatch ending lag with postpatch startup).
Shurikens are probably a top 5 projectile but not as exceptional as say, needles. His mobility IS exceptional, he has the best non-committal mobility in the game, but overall it's about as good as Pikachu, Sonic, ZSS' and Sheik's. They just commit a little harder with moves like Quick Attack and Spring Jump. The fact that Greninja doesn't need to commit to options like that is good but doesn't set him apart to "exceptional" level.
Greninja is "good" at everything and great at nothing, except his mobility which IS great but can be all but matched by better characters. He's a good example of a character with a versatility problem. It's enough to see him to the bottom of high tier but not much higher.
EDIT: You know, he's actually great at a lot of things. He has some fantastic traits, as you said. His dashgrab, range, recovery, they're all great. The real issue? He's not the BEST at anything. With his major tools neutered, nothing about him is unique.
Emblem Lord
IMO it comes down to no-one THAT good playing him in the US. Venia is starting to show promise at least. Across the pond you see istudying consistently getting 1st and 2nd in Netherlands nationals (Mr-R-dominated, but not a weak region) and Eddy just got top 8 in a German-French national, with Germany being probably the strongest region in Europe. Japanese results are decent, a few top 8s and 16s here and there with some smaller tournament wins.
It's concerning that he's not placing well in one of the strongest regions in the world but I can't blame the character for being underrepresented. You can say he's "underrepped for a reason" but he's not underrepped elsewhere and is definitely not a bad character, he's better than many mid/low tiers who get more rep than him. In weaker regions he places better than you'd expect for a lower high tier. Overall I'd say his results average out to about where they need to be for a top 15-20 character and I don't see many people argue he should be higher.