Not even entirely sure why people are implying Greninja will be useless in ubers because it's B- in the viability rankings there. Not very high but by god, it's viable
It's worth noting it plays an entirely different game in Ubers. While in OU, it's very powerful attacker with huge coverage, in Ubers, it's way too weak and frail. Instead, Greninja in Ubers is a Spikes lead that can defeat often used Ubers lead - Deoxys formes. If you try to use OU set, you will lose (although, considering how bad players in Ubers are, you can easily reach high places on the ladder with a bad team). Not that Ubers have meaning for OU. Deoxys-N is awful in Ubers, because other Deoxys formes are better, but that doesn't mean Deoxys-N isn't broken in OU (it is).
Anyway, to add something to the discussion. In BW metagame, one of threats was Mixed Attacker Hydreigon. It uses a set with great coverage (Dragon + Fighting coverage was great in BW, and Hydreigon usually also added Fire, Ground, and Dark attacks). It didn't have counters (well, okay, perhaps Chansey at full HP and Porygon2... sounds familiar?), although it had lots of checks. The issue was... it was slow, and 98 base speed made it outspeed by many OU threats.
Now, enter Greninja. It has good mixed offenses (yes, lower than Hydreigon, but with Protean it doesn't matter much), and way better speed of 122, so it would outspeed almost everything. It can easily use Gunk Shot and Ice Beam to cover against many threats. It also had two move slots to pick moves against other threats. Hate Scizor and Ferrothorn? Pick Hidden Power Fire. Hate Mega Venusaur, Keldeo, and Tentacruel? Pick Extrasensory. Hate Rotom-Wash and Manaphy? Get Hidden Power Grass. And so on, you have two moveslots to pick almost everything. When Hydreigon opted for Fire, Ground, and Dark coverage, Greninja has way more options to choose from, which may cause the opponent's check to be defeated, if right coverage was chosen. The opponent doesn't know what coverage was chosen, which makes using checks more dangerous.
I agree that Greninja is frail. But does it matter, when it outspeeds and OHKOes most of Pokemon, and it isn't frail enough to not survive a not-super effective priority hit (by the way, Greninja has Protean, so Mach Punch will be only super effective if Greninja had used Dark Pulse or Ice Beam, similarly with Bullet Punch). Hydreigon could have been easily defeated by outspeeding it with a good attack, but good luck outspeeding Greninja. Not to say that in Pokemon, Pokemons can switch, so seeing your check that somehow Greninja's moveset doesn't deal with, Greninja user can simply switch into appropriate counter for a threat, and continue to defeat your team while the Greninja check was dealt with.
Greninja is what BW Hydreigon would be if it had better speed and better coverage moves. In my opinion, it should be banned.