This is what I like for a Greninja.
Greninja@Life Orb.(Boosts the power of your moves,plus the Protean STAB)
Ability:Protean.(Gives you STAB no matter what attack you use.)
Nature:Modest/Mild/Quiet.(They all boost it's sp.attck,however Modest will lower Attack,that's why it's used more.Mild drops Defense, and Quiet drops Speed.)
Now for the moveset!
-Scald/Hydro Pump.(Scald has better accuracy, but a lower power of 80,but you can also possibly get a burn off on your target.Hydro pump has an accuracy of 80,meaning it may rarely miss,but when it doesn't it does a large 110 damage to whatever it hits!Plus STAB for both of these)
-Icebeam(Great accuracy of 100, nice damage of 90,with the ability Protean you can the STAB and your life orb,also a chance of freezing you target!Don't forget it's nice type coverage for flying,dragon,ground,and even grass!
-U-turn/Substitute .(Alright so mine has U-turn takes care of other Dark ,Psychic,and Grass types,not to mention decent power and great accuracy,and it also gets you lovely Greninja out of battle.Now substitute is something I tried out,with the hidden ability Protean,you'll more than likely,be constantly switching types ,thus making you sub last longer.)
-Dark Pulse/Extrasensory.(Dark pulse is used more but their pretty much the same moves just opposite types, they both do 80 damage ,both have 100 accuracy,and both have a chance of making you target flinch.Dark pulse would deal with Psychic,and Ghost types,while Extrasensory would deal with Poison,and Fighting types.)
I hope all that helps you decide!