You can go mixed, PHY, or SPA, but obviously his SPA and Speed is his best attributes.
The game is still fresh and people are still experimenting. I advise you to do the same, you never know what you might find--something different might work out for you.
Minus Nasty Plot, and a few of the TMs learned, I can confirm that he does indeed learn all of these:
http://pokemondb.net/pokedex/greninjaI myself have a Timid SPA Greninja and it works well, I'm using something like Dark Pulse, Surf (don't want to deal with missing, ever, and it's factually better than Hydro Pump now), Extrasensory, and Ice Beam. I figure it's pretty well rounded, and covers all the bases really. I haven't beaten the game yet like I said, so I can't verify all the TMs yet (I'm starting the Elite Four today).
To be honest, I don't think he's got the stats for mixed, but to each their own. I saw some people yesterday talking about how they enjoyed it, and I haven't tried it yet, so I can't really knock it. PHY seems pretty viable, with Water Shuriken being very nice itself, and access to things like Night Slash, Acrobatics (supposedly, can't verify), and Waterfall seem pretty good.
Anyway, I'm optimistic. Since I kinda rambled on a bit, I'll just say this: tl;dr - he's definitely a viable sweeper no matter how you make it, just experiment
