I've been running this set for a few days and it has hands down been the best physical Greninja set I've used. Special still outclasses it, but it is still good and unexpected.
Greninja (M) @ Dread Plate
Ability: Protean
EVs: 252 Atk / 252 Spd / 4 HP
Jolly Nature/Hasty Nature
- Acrobatics
- Fling
- Power-Up Punch/U-turn/Ice Beam/Hidden Power Ground
- Water Shuriken/Waterfall/U-turn
Okay, this looks super gimmicky, but it works. Acrobatics is really strong after Fling and is the strongest Physical attack that Greninja can use. It is a must on any set. Fling reaches 90 power when used with a plate + STAB and is Greninja's second-strongest physical attack (strongest with Iron Ball, but don't do that) and, like Acrobatics, has no immunities. For the remaining two moveslots, I have only used Power-up Punch and Water Shuriken so far, but the other slots help with dealing with some of Greninja's checks. Power-up Punch raises Greninja's mediocre attack and is useful since Greninja is able to force a lot of switches with its unpredictability. Water Shuriken priority is pretty helpful and has saved me a few times. It is a nice last resort move against faster Pokemon like Scarfers, Noivern, Jolteon, Aerodactyl, and others but is a bit weak. If you want strong Water STAB use Waterfall.
Unfortunately, this set has some 4 moveslot syndrome. I've often found that I missed U-turn a lot on this set and there were tons of times that I could have used it to my advantage. Going mixed would also be a good idea sometimes since Ice Beam has so much power and coverage and Hidden Power Ground covers the Electric, Steel and Rock type Pokemon that resist Acrobatics for super-effective damage and makes it immune to Electric-type attacks that will come at it when it is Water or Flying type. You could run Hydro Pump as well, but I'm not sure if it would be able to fit in the set. I'll do some more testing with the other options and come back for more feedback. Try it for yourselves. ^_^
EDIT: Oh calcs
+1 252 Atk Protean Greninja Acrobatics (110 BP) vs. 252 HP / 252+ Def Blissey: 393-463 (55 - 64.8%) -- guaranteed 2HKO after Leftovers recovery (Not that impressive considering Blissey could Thunder Wave and end the sweep. Chansey is an even worse situation. Also provides that you have used both Power-up Punch and Fling beforehand)
252 Atk Greninja Water Shuriken (3 hits) vs. 4 HP / 0 Def Mega Aerodactyl: 144-168 (47.6 - 55.6%) -- approx. 50.4% chance to 2HKO
+1 252 Atk Greninja Water Shuriken (4 hits) vs. 4 HP / 0 Def Mega Aerodactyl: 272-336 (90 - 111.2%) -- approx. 50% chance to OHKO
+1 252 Atk Protean Greninja Acrobatics (110 BP) vs. 252 HP / 0 Def Conkeldurr: 456-536 (110.1 - 129.4%) -- guaranteed OHKO (Probably wouldn't want to do this in fear of Mach Punch)
+1 252 Atk Protean Greninja Acrobatics (110 BP) vs. 4 HP / 0 Def Mega Charizard Y: 267-315 (89.5 - 105.7%) -- 37.5% chance to OHKO
252 Atk Dread Plate Greninja Fling (90 BP) vs. 252 HP / 0 Def Aegislash-Shield: 204-240 (62.9 - 74%) -- guaranteed 2HKO after Leftovers recovery (Not good enough...)
252 Atk Protean Greninja Acrobatics (55 BP) vs. 4 HP / 0 Def Alakazam: 135-160 (53.5 - 63.4%) -- guaranteed 2HKO (used in fear of Focus Blast)
252 Atk Protean Greninja Acrobatics (110 BP) vs. 4 HP / 0 Def Alakazam: 271-319 (107.5 - 126.5%) -- guaranteed OHKO
+1 252 Atk Greninja Water Shuriken (4 hits) vs. 4 HP / 0 Def Excadrill: 360-432 (99.4 - 119.3%) -- approx. 93.8% chance to OHKO
+1 252 Atk Greninja Water Shuriken (4 hits) vs. 252 HP / 0 Def Heatran: 224-272 (58 - 70.4%) -- guaranteed 2HKO after Leftovers recovery
+1 252 Atk Dread Plate Greninja Fling (90 BP) vs. 252 HP / 0 Def Heatran: 204-240 (52.8 - 62.1%) -- 98.8% chance to 2HKO after Leftovers recovery
252 Atk Protean Greninja Power-Up Punch vs. 32 HP / 0 Def Bisharp: 216-256 (77.4 - 91.7%) -- guaranteed 2HKO
252 Atk Greninja Acrobatics (110 BP) vs. 252 HP / 252+ Def Mega Venusaur: 182-216 (50 - 59.3%) -- guaranteed 2HKO
+2 252 Atk Greninja Acrobatics (110 BP) vs. 252 HP / 252+ Def Mega Venusaur: 360-426 (98.9 - 117%) -- 93.8% chance to OHKO
252 Atk Greninja Acrobatics (110 BP) vs. 252 HP / 0 Def Mega Venusaur: 242-288 (66.4 - 79.1%) -- guaranteed 2HKO
+1 252 Atk Greninja Acrobatics (110 BP) vs. 252 HP / 0 Def Mega Venusaur: 362-428 (99.4 - 117.5%) -- 93.8% chance to OHKO
4 SpA Mega Venusaur Sludge Bomb vs. 0 HP / 0 SpD Greninja: 153-181 (53.6 - 63.5%) -- guaranteed 2HKO
252+ SpA Mega Venusaur Sludge Bomb vs. 0 HP / 0 SpD Greninja: 205-243 (71.9 - 85.2%) -- guaranteed 2HKO
4 SpA Protean Greninja Ice Beam vs. 252 HP / 0 SpD Zapdos: 218-260 (56.7 - 67.7%) -- guaranteed 2HKO after Stealth Rock and Leftovers recovery (252 EV's will give you a 75% to OHKO after rocks :/)
4 SpA Protean Greninja Ice Beam vs. 4 HP / 0 SpD Zapdos: 218-260 (67.7 - 80.7%) -- 43.8% chance to OHKO after Stealth Rock
108 SpA Protean Greninja Ice Beam vs. 4 HP / 0 SpD Zapdos: 242-288 (75.1 - 89.4%) -- guaranteed OHKO after Stealth Rock (Hmm...)
4 SpA Greninja Ice Beam vs. 0 HP / 0 SpD Tornadus-T: 218-260 (72.9 - 86.9%) -- 81.3% chance to OHKO after Stealth Rock
4 SpA Greninja Ice Beam vs. 4 HP / 0 SpD Multiscale Dragonite: 200-236 (61.7 - 72.8%) -- guaranteed 2HKO (Switch out after this unless Dragonite does not use Dragon Dance)
88 SpA Protean Greninja Hidden Power Ground vs. 252 HP / 4 SpD Magnezone: 316-376 (91.8 - 109.3%) -- 50% chance to OHKO
4 SpA Protean Greninja Hidden Power Ground vs. 252 HP / 4 SpD Magnezone: 292-348 (84.8 - 101.1%) -- 6.3% chance to OHKO
188 SpA Protean Greninja Hidden Power Ground vs. 252 HP / 4 SpD Magnezone: 348-412 (101.1 - 119.7%) -- guaranteed OHKO
4 SpA Protean Greninja Hidden Power Ground vs. 4 HP / 0 SpD Magnezone: 292-348 (103.5 - 123.4%) -- guaranteed OHKO (Greninja outspeeds Scarfed Magnezone)
4 SpA Protean Greninja Hidden Power Ground vs. 32 HP / 0 SpD Bisharp: 180-212 (64.5 - 75.9%) -- guaranteed 2HKO
4 SpA Greninja Hidden Power Ground vs. 0 HP / 4 SpD Mega Manectric: 162-192 (57.6 - 68.3%) -- guaranteed 2HKO (on turn it Mega Evolves)
Sometimes Greninja just doesn't have enough power, but a few of these calcs surprise me. It's definitely not as consistent as the standard Special set, but still pretty good.