This is flawless:
252+ Atk Conkeldurr Mach Punch vs. 0 HP / 0 Def Greninja: 110-132 (74.8 - 89.7%) -- guaranteed 2HKO
This is yours:
252+ Atk Conkeldurr Mach Punch vs. 0 HP / 0 Def Greninja: 110-132 (76.3 - 91.6%) -- guaranteed 2HKO
Yours runs the risk of being killed by Mach Punch after taking LO recoil once. Flawless does not.
EDIT: Of course this is only really possible if you used Dark Pulse, because otherwise Mach Punch would do less.
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EDIT2: Jolly Scarf Garchomp also has a bigger chance to revenge kill you with Earthquake.
flawless:
252 Atk Garchomp Earthquake vs. 0 HP / 0 Def Greninja: 118-141 (80.2 - 95.9%) -- guaranteed 2HKO
flawed (25 HP IV):
252 Atk Garchomp Earthquake vs. 0 HP / 0 Def Greninja: 118-141 (81.9 - 97.9%) -- guaranteed 2HKO
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EDIT3: Unchoiced Talonflame likes this too.
flawless:
252+ Atk Talonflame Brave Bird vs. 0 HP / 0 Def Greninja: 114-135 (77.5 - 91.8%) -- guaranteed 2HKO
yours:
252+ Atk Talonflame Brave Bird vs. 0 HP / 0 Def Greninja: 114-135 (79.1 - 93.7%) -- guaranteed 2HKO
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Honestly, I don't think that Froakie is really worth it. After running some damage calcs, I can say that they don't look too promising...
All of this is in relation to Singles at level 50.