I don't know how many people have greninja experience...
But I have a little so here we go.
Mewtwo Pros
Combo game
Outspace
Hard to gimp
Can gimp greninja pretty easily
Cons
Light
Floaty
Greninja Pros
Fast kill options
Good approach options
Faster/better projectile
Fast recovery
Cons
Readable recovery
No real combos
I don't know a whole lot about the MU so sorry... You should try asking people on the Greninja boards to give their input!
Well it really shows that you don't know the MU, or really, anything about Greninja. No offense.
Greninja definitely has the upper hand in this MU. Mewtwo dies super early to Up-Smash (70% with no rage) plus we have ways of setting it up for a kill (D-Tilt and N-Air namely).
Not only that, it's easy to hit Mewtwo with most of combos in spite of him being so light because his hurtbox is big (not helping that his tail is still a hurtbox as well).
Mewtwo has very strong moves himself, but Greninja not being that light usually gives him better survivability than Mewtwo in most cases. Both characters have a killing Up-Throw though obviously Mewtwo's better.
Neither character can edgeguard the other very well, there's likely not going to be much offstage fight between them at all.
Confusion makes using fully charged shurikens a no-no. Uncharged ones are very good though and even if Mewtwo reflects them we don't really lose much, shurikens are also faster than Shadow Ball and so more spammable and they can also help prevent Mewtwo from charging it up.
Honestly... I don't think Mewtwo has much going for him here. I suppose his tail moves outspace us but he doesn't really get much out of them, Up-Tilt can combo into Up-Smash but that's just one thing.
Greninja has a better combo game, is faster, kills Mewtwo earlier than he kills him (being at around 65% is already death percent for Mewtwo, pretty much, especially factoring in rage), has a better projectile overall (though charged Shadow Ball needs to be respected). Mewtwo has better throws for killing and I guess better range on some moves and that's pretty much all I can think of.
I think this MU could be as bad as 65:35 in Greninja's favor honestly.