Regardless of whatever better kill options other characters have, no one has as many as Mario does while having that much mobility and dealing that much damage that quickly. Not being the best in the game at one thing is not a weakness.
Mario's recovery is entirely ungimpable and allows him to go deep enough to ledgedrop Fair (one of the strongest spikes in the game, with one of the best hitboxes) and recover.
Mario's range is moot when Bair outranges all of Mewtwo's options (and Mewtwo's got a lot of range), plus the fact that his top-tier mobility increases his effective range.
Mario's neutral is one of the best in the game. He has a projectile that is amazing at both approaching and forcing approaches, he has the least committing reflector in the game, and he is replete with moves that are safe on shield and perfect shield. If his neutral is bad, so is Sheik's.
His advantage and disadvantage states are also top 5 at least.
I could go on. But to rerail to the thread a bit, basically it's really bad for Mewtwo. Cape makes Shadow Ball a non-factor while also making Disable extremely risky. We have no answer for Bair. With how light we are, Mario may as well have Ness' Bthrow. Our janky hurtbox combined with Usmash's janky hitbox leads to gfycat-level absurd deaths, while he's short enough for SH Fair and Usmash to whiff. We can't gimp him. We can't land. We can't escape. If there's a worse matchup in the game, I couldn't name it (but chances are it involves Mario).
Mario's cape is far from unpunishable. If he reflects a shadow ball and you're standing at the correct distance, you can reflect
it back and he won't have time to reflect it back again, or even shield. And as long as you're not obvious with how you use
disable, you shouldn't be worrying too much about it getting reflected. Most of the time disable reflects happen
against those whose reflectors double as attacks (eg. Falco's, Ness baseball bat etc.) and happen by accident.
SH fair and usmash missing a standing Mario is kind of moot when you realize Mario spends about 70% of the match
in the air. Marios almost never approach from the ground unless it's to grab you. And even then, his shorthop is a bit
high which makes it a bit more difficult for him to apply pressure. Oh, and because his fair is so slow it's fairly obvious
when Mario will be going for a bair.
How do Fireballs force Mewtwo to approach? They fire fairly slowly so if Mario just sits back and throws them out
you can just charge a shadow ball while shielding every fireball that comes your way. Now you have a projectile
that will easily plow through his. He can try to reflect of course, but remember what I said about the ideal range.
As for approaching they can be a bit annoying, but doing so means he's facing you, and that means he can't use his
bair against you, and the rest of his options lose to good spacing (nair, dair) or are just too slow (fair).
Mario's options are only really safe if you respect them too much, that is, you sit in your shield in anticipation of
what he'll do and let him space or cross up your shield or let him grab you. The things you DO need to respect
are usmash and nair as a combo breaker. Oh yeah, because of his slow fair he's not very good at hitting Mewtwo
out of confusion or dthrow followups. As for landing against his usmash, he's
just slow enough that we can escape further
followups with a well-timed confusion, or escape with a teleport provided he doesn't anticipate it of course. Few characters
can challenge that headbutt directly, those being characters with very disjointed dairs like Link.
In short, you just have to stay light on your feet so that Mario can't get a solid bead on you, because despite what you may think
we do outspace him with our normals in general. Make a concerted effort to not let him get in your zone and you'll
be on the way to victory.
If you ask me, Fox is more difficult because he IS fast enough to make landing very difficult, his juggles are lethal
and he has annoying jab setups into kill moves. Plus he can easily dodge after reflecting.