Yeah, klefki is honestly better at getting up spikes.
However, greninja does have pros as a spiker. It can set up spikes on switches, and the sheer amount of switches that it forces is just scary. Almost all offensive pokemon in OU are threatened by one of his coverage moves, and to add on to that, you don't even know which moves he has and which moves he doesn't have. Greninja also beats basically every common defogger except for the rare empoleon. Greninja can't get up as many layers of spikes, but it's great at stopping them from being removed, and it can still have a great offensive presence even after it's set up 3 layers of spikes, whereas klefki can easily get up 3 layers of spikes by spamming t-wave, paralyzing everything, and then it can easily set up spikes, but it can't stop them from being removed eventually. Klefki does however have the perk of being able to stop most set up sweepers with prankster t-wave, but can't really do much back.
One cool thing about spikes lead greninja is that it basically guarantees 3 layers of spikes against lead rotom-w.
Scenario:
I lead with sash greninja, my opponent leads with rotom-w
I use spikes, turning me into a ground type, opponent uses volt switch, which greninja is now immune to
I use spikes again, opponent goes for hydro pump, I survive with sash
I set up the final layer of spikes, and then
hope that hydro pump misses greninja dies, but it's gotten up 3 layers of spikes.
(note: strategy does not work against people that try to hydro pump on the first turn)
3 layers of spikes is worth a dead greninja, because it's basically going to cost your opponent a turn to remove them, which can give you the crucial turn to set up and then start wrecking havoc with one of your set up sweepers.
I believe that
Doughboy had a cool spikes stacking RMT featuring spikes greninja, but that was during the XY meta. ORAS is a lot more fast paced, and greninja doesn't always have the opportunity to set up spikes.
So by now, I believe the only "true" counters to greninja now are P2, empoleon, chansey, and against non extrasensory greninja, tentacruel. Honestly, P2, empoleon and tentacruel are pretty bad, except for certain niches, leading me to believe that greninja is pretty centralizing. Offense got so buffed up this gen, with really strong megas literally made for HO, like mega gallade, mega lopunny,
mega salamence mega sceptile etc. They all work very well with greninja, and not to mention that greninja got low kick and gunk shot in ORAS, which allows it to hit it's original counters in XY.
tl;dr, greninja has merits as a spikes stacker, since it forces more switches, giving it the ability to set up spikes multiple times, it actually can do stuff and have offensive presence after it sets up spikes, and it can beat most common defoggers. Greninja is also a perfect fit for HO, because it's extremely fast and has a huge movepool to choose it's moves from.