It really depends on the context of your team and the Greninja's setup. I'll just show you an example of a setup I would use.
Greninja @ Choice Scarf/Expert Belt
EVs: 252 SAtk / 252 Spd / 4 Atk
- Hydro Pump/Scald
- Ice Beam
- Dark Pulse
This is what I would call a scout-sweeper Greninja. You could set it up differently to be better as a scout, but this is probably how I would run it. Hydro Pump is very high-power, but it has low PP and disappointing accuracy. On the other hand, Scald has decent power, high accuracy, and poses a possible burn to the opponent, which can seriously cripple a key team member. Remember that Greninja is very frail-- if it gets hit even once, it may be seriously hurt-- so I would personally choose power over accuracy. U-turn is definitely a plausible slot on Greninja, enabling it to retreat quickly. Ice Beam is for good type coverage, while Dark Pulse is a standard slot for the dual Dark-type. For item choice, go with either a Choice Scarf to get an edge on Speed, or run an Expert Belt to maximize super-effective damage (this would pair nicely with your Protean hidden ability).