STAB Ninja
Greninja@Expert Belt
Timid nature
Protean
252 Sp. Atk/252 Spd/4 HP
~Surf/Hydro Pump
~Dark Pulse
~Ice Beam/Blizzard
~Extrasensory
That's right, the Missingno. Master is back! And just in time for Generation VI, it seems, though I did miss out on contributing to Chesnaught and Delphox's analyses. But, oh well. Now, Greninja is easily the best of the three starters this time around in terms of sheer power and outright scariness. Hydro Pump, Dark Pulse, Blizzard, and Extrasensory have nice coverage, and more importantly, thanks to Greninja's Ability, it gets STAB on all of them.
Item further powers up super effective hits, and has personally worked well for me. As for the Ability, in addition to the aforementioned STAB on EVERYTHING, it's also useful to change Greninja's type in anticipation of an enemy attack. If you know you're not going to OHKO something that's going to go for a Fighting move, use Extrasensory so Greninja becomes a Psychic-type and resists it. I know it's frail, but believe me, sometimes it makes a difference.
Physical STAB Ninja
Greninja@Expert Belt
Adamant/Jolly nature
Protean
252 Atk/252 Spd/4 HP
~Water Shuriken
~Shadow Sneak
~Rock Slide
~Power-up Punch
Not quite as effective as its special attacking counterpart, but the option exists nevertheless. Greninja gets a pretty decent signature move in Water Shuriken, and as for why Shadow Sneak makes it in over Night Slash, it'll be exceptionally useful to be able to change Greninja to a Ghost-type. Immunity to Fighting is pretty decent. Other moves are for coverage, and in the case of Power-up Punch, also helps to boost that Attack stat.
Item and Ability have already been covered.
Other options:
*Greninja learns Acrobatics, which could be workable, but the Expert Belt is too useful to really get rid of.
*Another option is U-Turn, which could actually be worked into either set effectively enough.
*One of Greninja's Egg moves is Toxic Spikes, but let's be real here- Greninja's real strengths lie in hitting hard and fast. Supporting moves, not so much. It can't really afford to take many hits, so once you set up those two layers, that'll be pretty much it. Leave the Toxic Spikes to something with actual bulk.
Abilities:
*Torrent: When Greninja's HP goes below 1/3rd, its Water-type moves get a 50% boost. Not a bad Ability in and of itself, but... yeah, doesn't even come close to the sheer awesomeness of its Hidden Ability. There's really no reason to go for this over Protean.
*Protean: Greninja's Hidden Ability. Just before it attacks, Greninja changes its type to match the type of the move it's about to use. Basically, it gets STAB on everything. EVERYTHING. That alone should cement this Ability as one of the best ever as well as the reason why Greninja is the king of everything.
Partners:
Have a Greninja counter at the ready, because Greninja isn't exactly well-equipped for dealing with its own kind. Especially if you're running the special set- no super effective moves. Why it can't learn Focus Blast is beyond me... Also, you'll want something equipped with Rapid Spin or Defog for dealing with entry hazards.
Counters:
If you can outspeed Greninja, it won't be hard to deal with. Land a super effective hit before Protean has a chance to activate, and it's game over for Frogger here. That said, this may not be an option for physical variants,the ones that run several priority moves, but if you can predict what it'll do, that'll make it easier to deal with. Oh, and Sticky Web outright ruins it, so if you can set that up and prevent the opponent from removing it, you're good.
Opinion:
Greninja's become one of my most reliable Pokémon on random matchup, and not without reason. Besides its awesome Ability and beautiful stats, it looks cool. Though I generally advocate picking Chespin for in-game, one can't go wrong with Greninja for some serious battling.
Prediction for next week:
Slurpuff.