My main issue with Greninja has been that Sheik did everything Greninja did better (SHFF, aerials, combos, off stage gimps/KOs) minus the Hydro Pump gimp and USmash range. Actually Shurikens are pretty good being that they can net a KO at decent percents. Greninja is still fun and really cool, but from a competitive standpoint seems to be lacking at least reliable KO set ups post 100%.
Do you mean pre patch or post patch? Post patch I agree, Sheik outclasses Greninja in almost every aspect now. But before, it was a lot more even and I`d even say that Greninja was slightly better. Before I picked my main, the 2 characters I couldn`t decide between were Greninja and Sheik, so I made a comparison of all of their moves which I still have here:
Greninja vs Sheik (v 1.0.3)
Attack name...................Damage dealt............Damage needed to kill
Jab....................................10% vs 12%......................217% vs 185%
FTilt....................................6% vs 4%........................191% vs 214%
UTilt....................................4% vs 11%......................247% vs 219%
DTilt....................................7% vs 7%........................520% vs 275%
FSmash........................14-19% vs 13-18%...............93-60% vs 98-66%
USmash (sweet spot).....19-26% vs 15-21%...............94-59% vs 100-65%
USmash........................13-18% vs 11-15%.............104-69% vs 127-88%
DSmash (sweet spot)......11-15% vs 9-12%..............117-80% vs 123-91%
DSmash..........................9-12% vs 9-12%.............142-101% vs 123-91%
NAir...................................11% vs 8%........................173% vs 176%
FAir...................................14% vs 6.5%......................108% vs 148%
BAir.....................................9% vs 11%.......................165% vs 120%
UAir.....................................9% vs 8%.........................132% vs 136%
DAir.....................................8% vs 10%.......................223% vs 198%
B fully charged....................12% vs 7-11%....................105% vs 341%
B uncharged.........................3% vs 1%.........................520% vs 352%
Side B ..........................10-12% vs 12%...................109-90% vs 132%
Up B ...................................4% vs 12%.......................130% vs 109%
Down B .............................11% vs 12%........................88% vs 109%
FThrow.................................5% vs 7%........................514% vs 580%
BThrow.................................8% vs 7%........................214% vs 716%
UThrow.................................5% vs 5%........................175% vs 553%
DThrow.................................6% vs 6%........................461% vs 377%
Pummel................................2% vs 3%
So overall Greninja had much better smashes, especially Usmash, a better Jab that went through other jabs, a slightly better Uair, a much better Up B a better Side B and overall I`d say a better projectile as well.
While Sheik had much better Tilts (especially Ftilt), better aerials (especially Fair), a much better Down B and a much better grab game.
Regarding combos, Sheik could start them up more easily and they were harder to escape, but Greninja could deal more damage in fewer hits and had more damaging and more diverse combos. A single Greninja Usmash dealt as much damage as 5 Sheik Ftilts or 3 Fairs. So when Greninja did Utilt -> Usmash -> Usmash -> Uair at the start, it dealt as much damage as Sheik with her Fair -> 4 × Ftilt -> Grab -> Pummel -> Fthrow -> 3 × Fair combo.
And in off stage gimps these two were probably the best characters in the game. But I think that Greninja was better because its Bair gimped just as well as Sheik`s Bair and had more vertical range since it hit 3 times (upwards, in the middle and downwards). But Greninja also had the crazy Hydro Pump gimps which Sheik couldn`t match with Bouncing Fish or any other move. Even the Uair spike was easier to perform with Greninja because it had one more hit on its Uair which gave it more time to fast fall out of it. And thanks to its better recovery, Greninja could go deeper for the kill than Sheik.
That`s why I chose Greninja back then, but now might be a good time to get some practice in with my secondary Sheik as well.