Mewtwo is like the 4th easiest char to land the combo on. We all know this is a bad matchup. MK is small, combos easily, has a 0 to death and is fast and rushdown oriented. All things Mewtwo hates.
I might give a more detailed analysis later on, which is needed as this post doesn't really give any new information. Sorry about that.
That's a poor way of looking at it.
Yes, Mewtwo by character size is probably the 4th easiest character to continue the combo on once it begins. But that says nothing about how difficult it is to actually initiate the combo which is actually a really big deal!
With dtilt/jab/phasing/shadowball/landing mixups Mewtwo can play a ridiculously strong keep away game, possibly better than anyone except sheik. MK loves to get the dash attack either from neutral, or when trapping landings. Theres kind of no excuse for getting your landing caught by dash attack as Mewtwo, youve got the mobility, mixups and nair to cover yourself from this and more to the point you can easily just float around to the ledges, you are never forced to land in the centre of the stage.
Getting dash attacked in neutral at low %'s is again, almost entirely Mewtwos fault for not spacing with tilts and shadowball properly.
There is a VERY VERY big distinction to make between how difficult the combo is to start and how easy the character is to finish it off on.
For example, you might say that Olimar is really difficult to do the uair chain on, but he has no mixups on landings and a very punishable neutral game if he tries to stuff an approach.
Metaknight in general has a poor and punishable neutral game, Mewtwo absolutely smacks him in this regard. He can get some obnoxious KO's on Mewtwo and edgeguard fairly well to cover teleport but his 0 (or 30) -death ladder combo should not entirely be a problem because really, it is 100% the mewtwo players fault if they get caught in early %'s in the centre of the stage and get hit by dash attack. Many characters wish they could wall MK out and land as safely as Mewtwo to the point that I would say MK's ladder combo is not overly effective on Mewtwo because of how difficult it is to actually get it started.