M2's range is a bit worse than it seems at first. he does have disjoints, but all his moves actually extend his hurtbox a little. They combo better than most swordies and are a bit faster, so it is a pretty good tradeoff.
His bad double jump - specifically as an escape option - also comes back to haunt him in a few MUs. Having a uthrow 50/50 on him with shiek is great, and other characters put him in a bad spot even without a guaranteed 50.50 with uthrow.
Teleport makes his disadvantage reasonably good, but a hard read here can really hurt him with a strong grounded punish game.
Dtilt would be a massive wall, but it is low to the ground and therefor loses to jump ins. Not to mention the aforementioned hurtbox shifting because it isn't huge in most MUs, but someone like Marth with his dtilt can get weird f-smash kills because M2 poked forward a little.
Still, nair is incredible. This ties back into my last post, if you aren't SDIing m2's nair you deserve to die to it, full stop. You can pretty reasonably choose what side he spits you out on, which is enough for most characters to take a (strong) aerial punish rather than being footstooled and dying outright.
Something I am interested in is the new nair -> dair setup at the ledge. This seems like an absurdly high reward way to punish a ton of actions at the ledge, and if you drift intelligently you are usually pretty safe to use the nair to cover, say, a roll and still wind up not being punished.
Dair in general is pretty great. With the way his double jump works, you can kind of threaten a fair or uair and then dair them hard for dodging, which is great if you can land the sour hitbox because it will kill them vertically or horizontally, often when a spike wouldn't be that threatening. It has a huge hitbox and IIRC actually auto cancels from a short hop, which is a cool way to cover things like rolls with a strong punish while staying relatively safe.
Shadow ball is.... probably what makes m2 one of the best projectile characters in the game, combined with a reflector that is mobile, has great frame data, and actually punishes options that most reflectors lose to like shield. If you learn the way staling effects the ratios, you can learn when you are safe to reflect the shadow ball at a point where it is a moving deathball and will break reflectors, which is a cool answer to camping. The best reflector vs SB is actually palutena's, her low multiplier comes in handy here and she wins non staled, full charged shadow ball volleyball.
M2 is another character which I think you need to be able to c-bounce with. This kind of removes his weakness to cross up rolls in a few situations, because rolling into a mostly charged shadow ball is quite a losing situation.
Shadow ball is great against the shielding options that many choose. The ability to chase after a charged shadow ball was a great buff for mewtwo, if you land a fair on shield and have a fully charged shadow ball on deck, you can know that they can't shield anything and must roll to have a chance; running nair (ctick nair rant number 50 is coming soon!) covers tons of options in this situation and also doesn't have as much of a problem as just stuffing it.
Coming in backwards with a RAR is great, because the tail hitboxes are - for the most part - the best hitboxes m2 has. Plus when you are bad and often miss your cbounces like me, the b-reversed shadow ball can be a strong punish for anyone who wants to try and stuff your jump in.
The second jump helps m2 in a weird way as well. He can do SH Fair -> DJ instant fair, to hit a rising fair at ground level then quickly levitate to safety in the air. The safety of this varies greatly, some characters will hurt you for leaving the ground at all and then on triplats you are back to incredible safety, yet a hard read will hurt you bad. But, if you hit the rising fair you get a nice little string on the opponent, and m2's advantage is pretty freaking great with shadow balls and tilts covering landings quite well.
Shadow ball also gives him great mobility, Wadi exploits this very well. It really ties his kit together in a number of ways because he is a character that would get bodied by shield camping without it. Speaking of which, you can also patch this up and give m2 a pretty solid grab game by learning how to do the roll canceled grab consistently. The extra range is a huge addition to his rather poor range, just look at how jump canceled grabs can zone break in melee to get an idea of how powerful it is to suddenly be grabbing.
But... worst MUs are Diddy, Cloud, and Shiek... you really see why he isn't that popular despite all the above positives. Still, with DLC being stronger now than before he appreciates the decline in Diddy popularity; assuming my scene is like others many of the Diddies are now bayos and he seems to prefer this decently. YOU BETTER HAVE GOOD SDI, and even then it isn't always possible to not get laddered.
I am unsure on M2, I always felt he had a better Diddy MU than we all thought. Perhaps if you could reasonably escape dtilt usmash, even a third of the time, you might find this is not so bad. Especially since at the ledge you have mobility and great options, an amazing projectile, and you aren't in danger of dying until dtilt -bair starts being a threat.
None of the above is groundbreaking or even new, but that is what comes to mind when someone says M2.