I'll add my scrubby two cents on MK. Meta knight is not that fast, and although he has many jumps, he still has no projectile and that stick he calls a sword does give some range, but not enough to be anything but an up close, melee character. The main moves to watch out for are dash attack, dash grab, and uair. Obviously in the neutral it is pretty easy to run away from MK and spam shurikens, but when he's up close, our superior mobility and aerial range is key. Spaced/retreating Fair should be sufficient to catch many of the dash attacks they love to throw out. And due to Grenina's light weight and Shadow sneak, Greninja has the best tools out of any character to get out of Meta Knight's main kill setup --Uairs to up B. We can SS out of Uair up to 38%, so his 0-death setups straight up will not work against a knowledgable greninja. Also, we can SS out of the first hit of shuttle loop as long as it's not sweetspotted. Although we may take some good damage from the combos, our tools to get out of them, even with the bair jablock, are some of the best in the game. Along with his lack of spike or jank options aside from Uair, meta knight should pretty much never get early kills on greninja.
Furthermore, because of shurikens and mobility, meta knight will literally always be approaching us. However, this is not all meta knight has. Greninja must be careful not to land unsafely in front of meta knight, as he has many close up kill setups, such as Dtilt to dimensional cape and raw up b oos. But overall if you cross him up or space him well enough, he should have to rely on mixups or hard reads to kill you (like dimensional cape as you throw a shuriken, or his surprisingly good upsmash.) Offstage, he can edgeguard us fairly well with bair, dair, and nair due to our lack of hitbox, but in all likelihood his edgeguarding should not kill us because of our ability to mix up hydro pump angles and SS and the fact that he just doesn't have any or powerful semispike moves.As long as we are ready to tech stage spikes, recovering should not be too much of a problem. Against Meta knight's options, Greninja must read which option MK will use- Side B, Down B, or Up B. We can Hydro pump up B and side B fairly easily, and MK's low horizontal air mobility afterwards makes it a pretty good option to get the kill. maybe one follow up will be necessary. Dimensional cape can be 2-framed by bair, which MK can tech.
Landing should not be a problem for greninja either. MK's Uairs are dangerous, but our ability to get out of uairs and up B is a lot better than other characters'. Our ability to just hydro pump somewhere else on stage, landing nair, etc. make our landing options good against him. However, when he is landing, he can dimensional cape to the ground or to a platform, and his many jumps help, but if MK decides to be aggressive, Greninja's Usmash stuffs dair, nair, etc. and Utilt stuff out his aerials well enough due to invincibility.
As long as Greninja plays defensively with lots of Fair and good spacing, MK should have to rely on too many mixups and reads for this to be even. Greninja's projectile and superior mobility give Greninja the advantage in the medium and long range, while his escape options severely limit MK's reward up close (where greninja doesn't do too bad himself). Overall I would label this 55-45 Greninja's favor.