I prefer a special set to a physical for Greninja. I've been testing a lot and he cleans up well with this:
Greninja @ Life Orb
Ability: Protean
Shiny: Yes
EVs: 252 Spd / 252 SAtk / 4 HP
Timid Nature
- Water Shuriken
- Ice Beam
- Hydro Pump
- Dark Pulse
(Water shuriken for when he can't outspeed and just needs to finish something off)
the only disadvantage of this set is that unless you use hydro pump, which has already been nerfed, your typing remains weak to fighting moves
If you have a Physical move, then the last 4 EVs should go to Attack and you shouldn't be using the Timid Nature. Also, it's been said that Greninja only needs 244 Spe EVs and 168 SpA EVs to outspeed and OHKO a majority of targets. The rest can go into Atk if you're running a physical move.
Water Shuriken is a pretty bad move without max Attack investment, considering Greninja's already sub-par attack. It fails to OHKO/2HKO anyone you would use it on, such as Blaziken and Talonflame (4 Atk (custom) (Water Shuriken hits 3 times) vs. 192 HP / 0 Def (custom): 126-150 (36.52 - 43.47%) -- guaranteed 3HKO). Dark Pulse is also a sub-par option as it only really helps you take out spinblockers, as Hydropump will almost definitely do just as much damage to any other ghosts (Like Gengar: 168 SpA Life Orb (custom) Hydro Pump vs. 0 HP / 0 SpD Gengar: 255-302 (97.7 - 115.7%) -- 87.5% chance to OHKO). U-Turn is better used for taking out Psychics like Celebi, Alakazam, Espeon, etc. as it KO's and gives your team momentum. Lastly, HP Fire is amazing as it stops you from being walled by the likes of Scizor, Ferrothorn, etc. and Grass Knot is also great in the same regard for bulky waters.
Overall the best set for Greninja is probably:
Greninja@Life Orb
Protean
Naive/Hasty, 96 Atk / 168 SpA / 244 Spe
- Hydro Pump
- U-Turn
- Ice Beam
- HP Fire / Grass Knot
This is VCrowe's set, here are some calcs from them:
168 SpA Life Orb (custom) Hidden Power Fire vs. 252 HP / 216 SpD Scizor: 442-530 (128.48 - 154.06%) -- guaranteed OHKO
168 SpA Life Orb (custom) Ice Beam vs. 252 HP / 0 SpD Latias: 257-304 (70.6 - 83.51%) -- guaranteed 2HKO
100 Atk Life Orb (custom) U-turn vs. 192 HP / 64 Def Reuniclus: 244-291 (59.65 - 71.14%) -- guaranteed 2HKO
100 Atk Life Orb (custom) U-turn vs. 4 HP / 0 Def Mew: 211-250 (61.69 - 73.09%) -- guaranteed 2HKO
168 SpA Life Orb (custom) Hidden Power Fire vs. 172 HP / 0 SpD Abomasnow: 468-551 (128.57 - 151.37%) -- guaranteed OHKO
168 SpA Life Orb (custom) Ice Beam vs. 252 HP / 4 SpD Dragonite: 608-717 (157.51 - 185.75%) -- guaranteed OHKO after Stealth Rocks
96 Atk Life Orb (custom) U-turn vs. 252 HP / 4 Def Espeon: 312-369 (93.41 - 110.47%) -- 62.5% chance to OHKO
168 SpA Life Orb (custom) Hidden Power Fire vs. 252 HP / 208 SpD Ferrothorn: 302-359 (85.79 - 101.98%) -- 6.25% chance to OHKO
168 SpA Life Orb (custom) Hidden Power Fire vs. 252 HP / 4 SpD Forretress: 614-723 (173.44 - 204.23%) -- guaranteed OHKO
168 SpA Life Orb (custom) Ice Beam vs. 4 HP / 0 SpD Garchomp: 702-827 (196.08 - 231%) -- guaranteed OHKO
168 SpA Life Orb (custom) Ice Beam vs. 244 HP / 0 SpD Gliscor: 769-910 (218.46 - 258.52%) -- guaranteed OHKO
168 SpA Life Orb (custom) Hydro Pump vs. 0 HP / 4 SpD Heatran: 351-416 (108.66 - 128.79%) -- guaranteed OHKO
168 SpA Life Orb (custom) Ice Beam vs. 4 HP / 0 SpD Hydreigon: 330-393 (101.22 - 120.55%) -- guaranteed OHKO
168 SpA Life Orb (custom) Ice Beam vs. 248 HP / 0- SpD Landorus-T: 811-957 (212.86 - 251.18%) -- guaranteed OHKO
168 SpA Life Orb (custom) Hydro Pump vs. 72 HP / 0 SpD Chandelure: 406-478 (145.51 - 171.32%) -- guaranteed OHKO
96 Atk Life Orb (custom) Shadow Sneak vs. 4 HP / 0 Def Espeon: 179-213 (65.8 - 78.3%) -- guaranteed 2HKO
168 SpA Life Orb (custom) Ice Beam vs. 0 HP / 4 SpD Latios: 281-330 (93.35 - 109.63%) -- 56.25% chance to OHKO
96 Atk Life Orb (custom) U-turn vs. 0 HP / 4 Def Celebi: 421-499 (123.46 - 146.33%) -- guaranteed OHKO
**Some of these calcs have 100 Atk instead of 96 but that should barely hurt the KO's at all.**