252 SpA Life Orb Protean Greninja Grass Knot (20 BP) vs. 252 HP / 0 SpD Rotom-W: 70-86 (23 - 28.2%) -- possible 5HKO after Leftovers recovery
That's a calc with the standard Rotom-W Defensive Pivot Set, however, this is pre-ORAS, with Max SpA Timid.
If you take into account that most run 44 Atk:
212 SpA Life Orb Protean Greninja Grass Knot (20 BP) vs. 252 HP / 0 SpD Rotom-W: 65-81 (21.3 - 26.6%) -- possible 5HKO after Leftovers recovery
Seems like a nice check? The low damage is mostly due to Rotom-W's infinitesimal weight. Now, try the same with HP Grass.
Pre-ORAS Greninja:
252 SpA Life Orb Protean Greninja Hidden Power Grass vs. 252 HP / 0 SpD Rotom-W: 205-244 (67.4 - 80.2%) -- guaranteed 2HKO after Leftovers recovery
Post-ORAS Greninja:
212 SpA Life Orb Protean Greninja Hidden Power Grass vs. 252 HP / 0 SpD Rotom-W: 198-237 (65.1 - 77.9%) -- guaranteed 2HKO after Leftovers recovery
The other problem that arises is how can Rotom-W retaliate to a Grass type Greninja?
Also, as an aside, I think Naive is usually chosen, because the usual way to take care of Greninja is to use priority Mach Punch from Loom/AV Conkeldurr, and you need the extra defense to avoid the guaranteed OHKO from a Jolly Loom's Mach Punch. That is unless the Greninja carries Shadow Sneak