Greninja @ Life Orb
Ability: Protean
EVs: 4 Atk / 252 SpA / 252 Spe
Hasty Nature
- Water Shuriken
- Hydro Cannon
- Taunt / other
- Extrasensory / Gunk Shot / other
This may look a weird set, but it does well against a number of pokemon that would normally beat it.
Firstly, water shuriken is a useful move against a number of pokemon. FEAR straight-up dies to it when otherwise it would probably win. things like Mega Aggron also lose to it, with water shuriken breaking sturdy and the multi-hit nature of the move meaning that metal burst does very little in return. Using this to knock it into hydro cannon range then KOing works well against a mon that otherwise counters. The priority and sub-breaking abilities also make it nice vs. encore/disable mega alakazam which can be a nuisance for greninja sets as well.
Hydro Cannon hits hard, which is something Greninja really needs when it's relying on a mere 103 base SpA. Hydro Pump is usable but in many cases far worse. For example, Greninja has no chance against Mega Mawile when using Hydro Pump, whereas with Hydro Cannon it has a chance to KO: 252 SpA Life Orb Protean Greninja Hydro Pump vs. 252 HP / 0 SpD Mega Mawile: 285-335 (93.7 - 110.1%) -- 62.5% chance to OHKO
It's also worth noting that water shuriken can be used to outplay sucker punch and bring it into OHKO range even on a min roll with two hits, though sucker punch barely 2HKOs in any case.
The last two moves should be considered together, as neither on its own does particularly much alone. Taunt is useful in shutting down otherwise annoying pokemon such as whimsicott (which often goes for sub first and can wait for a gunk shot miss). It also stops things like Mega Venusaur from going for sleep powder, allowing extrasensory to give greninja a chance at beating it. Gunk Shot alongside taunt allows Greninja to beat things like Perish Song Azumarill whereas with only gunk shot, greninja has to rely on a roll and two hits and azu not getting a triple protect, which adds up to a far-from-perfect success chance.
Both extrasensory and gunk shot allow greninja to beat zard y if predicted correctly, as the change of type stops solarbeam from KOing and the damage from these moves followed by hydro cannon will KO. Be warned however that fire blast will OHKO after the type change, though it won't beforehand so if Fire Blast is predicted then Greninja should use water shuriken first, which gives a favourable roll to KO even with just two hits.
Other options for the last move include Dark Pulse, which alongside taunt allows greninja to beat most Deoxys-D; Ice Beam, which allows Greninja to beat Dragonite, Rock Slide which gives an easier win against Mega Charizard Y, and even things like Hidden Power Fire to beat ferrothorn or scizor if they become problems for the team. Low Kick alongside maximum attack investment can do nice work against Chansey alongside taunt, as well. Increasing HP investment to let it live 3 seismic tosses after LO recoil.
The set's main niche isn't in beating a lot of things, but rather beating opposing pokemon that would normally expect to win in this matchup. On a crowded ladder or in a tournament where you don't often play the same people multiple times this is useful, as an opponent expecting an simple win can be outpredicted with ease. The set is also very useful in covering up weaknesses that your other pokemon leave: It's easy to stick two very powerful pokemon on a team, but this often leaves the problem of three or four pokemon you're weak to that are difficult to beat all in one pokemon. Being able to take care of Rhyperior, Aggron, perish song Azumarill and FEAR all in one set is very useful at times, even if not particularly powerful on its own.