The things is with Greninja is that it got banned due to its high speed and near perfect offenses(Protean+Life Orb.) Being as your Greninja is Mild nature, you won't get much use out of it because of that immense drop in speed. Granted most Uber Pokemon are slower than it, it does help to have an edge in the form of speed. I'd suggest either breeding for a Timid natured one, or just hope Greninja is faster than the Pokemon you'll face. I'd suggest the standard offensive set, as this In-Game, and not the Uber tier.
Greninja@ Life Orb
EVs: 40 Atk / 212 SAtk / 252 Spd
~ Hydro Pump
~ Ice Beam
~ Gunk Shot
~ Dark Pulse/Extrasensory
This was the set that gave Greninja a death sentence. Gunk Shot for those pesky Fairies, destroying them thinking they'd wall you. Ice Beam covers Dragons and such. Hydro Pump is Greninja's strongest viable option(Hydro Cannon sucks), and the last move is up to what coverage you prefer. Extrasensory beats out MVenusaur, where as Dark coverage is really good this generation. Mind you that you will not get the exact successful results being as you have that Mild Nature.