Mewtwo is back and now he’s up against the Pokemon who replaced him in Super Smash. Needless to say, this will not be a close fight! Greninja may be swift and powerful, but Mewtwo surpasses him in both areas. Greninja simply doesn’t have a chance against the ultimate Pokemon. Mewtwo even has a Mega form, which increases his abilities even further. In that form, he’s easily the strongest Pokemon in existence! Mewtwo wins.
DReager1.com 
Mewtwo is maybe my favourite pokemon (I loved Kabutops too). Whoever voted for Greninja need to get their eyes checked lol just because Greninja is part dark-type and has a type advantage doesn’t mean he’s gonna beat THE ULTIMATE POKEMON MEWTWO!!! lolz. Mewtwo was created to be the most powerful pokemon of all time and he’s still up there (and still may be the best but annoying rubbish pokemon like Arceus and Mega Rayquaza are stealing the show at the moment). Greninja doesn’t have a chance against Mewtwo when Mewtwo is on his A game.
If we’re going to talk about pokemon game stats (excluding smash) then:
MEWTWO THE MOST POWERFUL POKE Cool Ninja frog with erm…a scarf-like tongue?!
Hp = 106 Hp = 72
Attack = 110 Attack = 95
Defense = 90 Defense = 67
Special Attack = 154 (highest of all legendaries) Special Attack = 103
Special Defense = 90 Special Defense = 71
Speed = 130 (quickest of all legendaries) Speed = 122
So as you can see, Mewtwo OWNS Greninja in every department. Yeah I wish smash Mewtwo was as excellent as Pokémon game Mewtwo but that’s not gonna happen sadly. Yeah in smash, Greninja might be better than Mewtwo but in a true battle…MEWTWO OWNS.
Absolutely, Mewtwo basically has every advantage in this fight. I personally consider him to still be stronger than Arceus and the others, but they would make it a nice fight. I can’t wait to play as Mewtwo in Pokken, hopefully he’ll really get to show his stuff there and leave as a heavy weight.