I’d like to see your reasoning, actually, if only to see a little more Greninja in this thread.
First off, I do think the MU is close & Mario definitely has harder MUs to deal with (Sonic for example), but Greninja's strengths in the MU (especially neutral) push it away slightly from just calling it another even in my opinion. Ally/Anti both were hesitant about it but I've seen them change their opinion a lot over time & actually play the MU more at a high level as well. Not just them either, Elexiao/iStudying consistently beat Supahsemmie who is 4th on Dutch PR & Japanese Greninja's got multiple set wins over FILIP, Ron & bAhuto as well just in case people think I'm talking out of my ass lol. I've thought this for awhile.
Let's see what aspects of play Mario dislikes in a character or dislikes dealing with in general: Disjoints/Range, Good Jugglers, Fast or Campy Chars, Evasion (Hard to Grab/Land Kill Moves), etc. Greninja encompasses all of this. It's not as extreme walling out as Cloud, or necessarily as speedy as Sonic in certain areas but he has both combined into one character along with his other tools that make it uphill. For Greninja, Mario can be played around & he doesn't need to even challenge Mario's frame data up close all the time either. He has no reason to and Mario can't force him to play & box up close like that. It's easier for Greninja to get a lead first & maintain it to force Mario to come to him rather than the other way around from the start of the match.
Greninja's excellent mobility attributes in all aspects alone is an issue for Mario in neutral to deal with as he's heavily outpaced & this allows Greninja to dictate a lot of how the game plays out because of it; especially when he has a better projectile & more range. Greninja's F-tilt is safe when spaced & serves as a grounded poke that outranges Mario's ground game completely. UpTilt is disjointed & beats out all of Mario's landing options or jump-ins cleanly as it can't be challenged. Fair is another disjoint & despite its startup, in combination with his air drift/mobility he has no trouble still getting it out & it's an issue because Mario can't punish it when spaced properly so it's free pressure; not to mention how he can mix it in w/ empty hops to bait Mario to commit or catch roll-ins as he retreats. And if he ever has to contest Mario in the air up close, he has his Frame 5 Bair with decent range to challenge him with.
In regards to playing around Mario on the ground however, he can still toss shurikens, use his quick Jab/Ftilt or Dtilt while pivoting or crawling back respectively, use his long-range pivot grab to snag aggressive approaches or angle hydro pump back to give him room. He walks so much faster (which is great because it retains access to his whole kit that stuffs out well) to where Mario's ground game isn't an issue & if Mario wants to keep up, he's going to need to jump more often which opens up room for exploitation.
Cape is barely an issue for Greninja to deal with, all it does it make him not be able to fully charge shurikens as much as he could in other MUs. He can still toss them & mixing up shuriken charge timings can go a long way; any mistiming on cape gets Mario hit. It can be baited out with good movement too. Mixing in b-reverse, wavebounce, c-bounce, etc & he def won't be able to cape them all. It has a bit of end-lag to it that Greninja can punish with his speed for a dash grab/attack if mistimed or he can keep charging to hit early capes. All of this gives Greninja more control than one would think, he
wants Mario to always be wary of shurikens regardless & overuse of cape will do the opposite of help & will just give him openings to get his advantage state going.
Fireballs are fine to deal with whether Gren uses an aerial to hit through it & possibly hit Mario too such as retreating Bair or an aggressive Nair, jumps over it so the Mario can't follow it to grab, or clanks it with uncharged shurikens or jab. If Greninja is already cornered, he can substitute out of the situation or push an approaching Mario who is following the fireball arc away with Hydro Pump. If they jump & spam fireballs, he can run under their arc & punish lag.
Mario can't keep Greninja in one place for long. If Greninja doesn't want to be cornered, he'll get himself out. When Mario attempts to, Gren can use his high jump & good airspeed or HP angles to escape as Mario's mobility isn't enough to reach in time & he can reset the situation from there to go right back to playing in neutral where he has the upper hand. Same with just jumping away once Mario puts him in disadvantage or pressures him.
As long as Greninja doesn't shield too often (instead abuse his low profile & mobility to not let Mario Bair pressure for free) when he doesn't have to or let Mario freely run up & grab after fireballs or Bair pokes, he'll be fine. Gren can run under (or crouch) misspaced Bair or dash under Mario's hops & cross him up, walk/jump away from pressure which Mario can't really chase with his lacking speed in comparison, or just UpTilt jump-ins anytime Mario is in the air.
Mario has decent kill power but is lacking in kill setups as the percents rise (at least ones he'll reliably catch Greninja with as he dances around) & he can struggle to hit or grab Greninja as is to finish the stock. If Greninja isn't platform camping or shuriken camping until Uthrow %, he can get confirms off of bad approaches from Mario such as ducking a high Bair and landing Up-Tilt Uair, outranging approaches w/ pivot grab, or whiff punishing an approach with Nair/Dtilt to confirm into Usmash among a list of other things he can do.
Both characters combo each other pretty solidly once they get in but the main catch is how Greninja can keep his own advantage state going longer than Mario because he can still chase landings or reset juggles harder. He has ways to mitigate damage too whether through Mario not being able to uptilt at lower %s cause Gren can hold down & shield because he's a fast-faller, SSHC which can hit Mario back or be safer because there's a platform above or Gren's high jump that allows him to disengage from situations (the same thing at late %s where Mario's combos lessen & Greninja can just jump away & mix up his landing w/ Hydro Pump to end Mario's advantage state immediately).
CONCLUSION: What all of this means is that while their advantage states when done properly seem to relatively even themselves out (although after awhile Mario's stuff doesn't work as well as %s climb and Greninja gains more kill confirms), Greninja does better in disadvantage state than Mario with how well he can escape or be hard to hit & Greninja also has the upper hand in neutral which gives him more control. This makes it more difficult for Mario than people give Greninja credit for & Gren gets away with too much and has too much freedom because of the speed difference. He can close out stocks better than Mario as long as he doesn't land on Mario at kill % or hop in his face, and if he gets a lead, he can honestly rival Sonic in the way he can run away from people and camp/time them out.
