Cloud is weird in that he likes to charge his Limit Break and Mewtwo likes to charge his shadow ball, so both can tempt the other to approach but in a way Cloud could potentially get better payoff from it, since his side b limit break can kill Mewtwo early and that's pretty harsh.
But on the other side of the coin, Mewtwo has it made fighting Cloud. Our neutral is a lot more rewarding and Cloud isnt safe in shield, nor safe rolling around because of Shadow Ball. Cloud is a bit more defensive in 1v1 because he needs to charge limit before he can come charging in on anybody, and he likes to have some distance so his sword is relevant, but Mewtwo can get in and not worry about Clouds range, nor does he have to worry about defensive Cloud because we have an answer whether it'd be a grab, shadow ball, nair or simply a dash attack after reading a roll. If he tries to roll behind us, we can read that with a bair, too. There's not a lot of room for error so the opponent would need to mix up their defensive options quite a bit to get past us.
Mewtwo has much faster aerials than Cloud and I think this will help in the long run. Yes, Cloud has a fast uair, but its not strong anymore so Mewtwo doesnt worry about it, not to mention if we can go undernearth the hitbox we can just fair to punish the long animation of his uair. These are just possibilities, keep in mind.
Should also be mentioned Mewtwo has significantly better grab game than Cloud, so we will have better options than he does right off the bat. We also have a command grab and reflector, which renders his shield even more useless, and his projectile ultimately meaningless.
We also gimp the living crap out of him. The only think he could probably do to stop us is nair (maybe?), or up b spike us lmfao. He is almost as bad as Ganon when it comes to gimp protection.
The only things we should be worried about are his smashes, nair and his limit being charged. Cloud has 2 pretty solid smashes for fighting Mewtwo (usmash and dsmash), one of them potentially killing us somewhat early while the other would just be good for damage. Nair is fast and with limit break charged he can go full out Shulk 2.0 on us, which isnt fun even with our new found weight. We can do a few things to fight it off, but if he gets in there once, hes bound to string them. Limit break in general is also kind of scary, as I said he can kill Mewtwo pretty early with side b limit but he needs to have the opportunity knock. Even more scary though is the speed boost he gets from charged limit. This gives him a bit more mobility that Mewtwo would rather someone not have at all, but I mean hey, what can you do?
Oh yeah, and Cloud with his weight and fall speed is a perfect victim to our jab strings, including jab to down b, my personal favourite.
Honestly I would put this matchup at 60:40 in Mewtwo's favor, I wouldn't say that is stretching it considering most of our options arent shut down by Cloud, but yet his options are much more limited whether in neutral, off stage, or just between strings. This is a MU that I think a lot of Cloud mains sleep on, as well (for as much as that is cliche to say right now).