Scizor rarely threatens Greninja, but Ferrothorn is acknowledged. Overall, I find U-turn/Dark Pulse/Hydro Pump/Ice Beam to be useful in more battles, even with Ferrothorn present, as the ubiquitous Aegislash all but necessitates Greninja's strongest coverage move against it (Greninja can't even 2HKO Aegislash 1-on-1 with HP Fire), and U-turn is basically free damage on checks where coverage can't help you.
His Hidden Power options are just about all inferior to his non-Hidden Power options, and he gets STAB on those too. The only one of any real use is Hidden Power Fire for Ferrothorn. Once the Pokebank is available, Dark Pulse is only going to get better with Jirachi running around.
All of this fluff to make no point. Greninja covers just about every Pokemon in the game with Dark/Ice/Water/U-turn coverage, with strong Grass and Psychic coverage if it is ever needed. Fire for Ferrothorn has already been covered, so what other options do you have with HP that aren't useless? HP Steel? Fight? Fairy? Every other HP is just a horrible move that Greninja doesn't ever need to use.
Dark Pulse, on the other hand, is one of Greninja's most effective moves. It has respectable BP, great neutral coverage, and surprising utility for some of the more obscure but still useful Ghosts and Psychics (like Deo-D and Mew) with the bonus of actually beating Aegislash. It's a more reliable move to toss out than Grass Knot or HP Fire by a longshot, and can deal good damage on a lot of Pokemon when combined with U-turn.
And lol @ bulky Waters. The bulky Water of choice is currently Rotom-W and none of Greninja's viable options hit it harder than Dark Pulse -> U-turn.
Man I'm glad I skipped the first part to read your reply to me, when I went back and read the top it was clearly saving the best for last. This is Bulky SD Scizor with barely any investment:
40+ Atk Technician Scizor Bug Bite vs. 0 HP / 0 Def (custom): 66-78 (23.15 - 27.36%) -- possible 4HKO
If you U-Turn out, you're taking at minimum 35% HP from a Bullet Punch. The only move you can use safely will be Hydro Pump if you stay in, because if you use Dark Pulse or Ice Beam then Scizor is going to OHKO you with every single move in his moveslot on most sets. Hydro Pump does 41.27 - 48.83% to him if he is Bulky SD, which will 3HKO him. At best, you are both going to kill each other due to LO recoil.
And god forbid he is a more offensive Scizor. Also, this isn't even mentioning the revenge kill potential, a more offensive Scizor can take you down for free if you use Ice Beam prior to the switch in, and generally 2HKO you in all other cases. Your only true hope against a Scizor is to use HP Fire, or switch out without using U-Turn.
Your point about Greninja not being able to 2HKO Aegislash is irrelevant, because even an unboosted and uninvested Sacred Sword will kill OHKO you in return if you use Dark Pulse. I'm too lazy to do the calc, but if a 90 BP move can't even 2HKO (As you say), then there is no way that a 120 BP move will OHKO, considering that both are super effective. So if you use Dark Pulse, you die instantly to Aegislash. Not to mention you shouldn't be trying to fight Aegislash with Greninja in the first place, but if you have to at some point, HP Fire will at least let you put some good damage on before croaking (pun intended).
HP Fire hits Ferrothorn, Scizor, and basically anything Steel besides Heatran. As for Jirachi:
252 SpA Life Orb (custom) Hidden Power Fire vs. 252 HP / 236+ SpD Jirachi: 166-198 (41.08 - 49%) -- guaranteed 3HKO
252 SpA Life Orb (custom) Dark Pulse vs. 252 HP / 236+ SpD Jirachi: 190-226 (47.02 - 55.94%) -- 18.75% chance to 2HKO
Dark Pulse only KO's Jirachi faster 19% of the time, I'd say the huge coverage gained from HP Fire is worth that.
U-Turn + Hydro Pump can hit basically everything that Dark Pulse hits for the same or near OHKO. Nothing will hit bulky steels or waters as hard as HP Fire/Grass Knot.
"And lol @" being so ignorant as to think that just because Rotom-W is prevalent in the meta game that no other dangerous bulky waters exist.
Even if Rotom-W was the only water I was talking about:
252 SpA Life Orb (custom) Dark Pulse vs. 248 HP / 232+ SpD Rotom-W: 91-109 (30.03 - 35.97%) -- guaranteed 4HKO
4 Atk Life Orb (custom) U-turn vs. 248 HP / 0 Def Rotom-W: 52-62 (17.16 - 20.46%) -- possible 7HKO
So that is 47.19 - 56.43% over two turns.
252 SpA Life Orb (custom) Hidden Power Grass vs. 248 HP / 232+ SpD Rotom-W: 159-190 (52.47 - 62.7%) -- 99.61% chance to 2HKO
Shroomisaur just brought up using HP Grass as a surprise for Rotom-W, and it is also effective at murdering a lot of the threats that Grass Knot is used for.
I typed all this up, but honestly your argument was pretty invalid after you said "Scizor rarely threatens Greninja".
TL;DR: Use Dark Pulse or U-Turn, not both. The benefits/coverage/OHKOs are similar when used with Hydro Pump, and using them both will take away valuable grass/fire coverage.