One awful MU is Yoshi for sure. That character does just an awesome job at putting out pressure at different ranges, unless I'm directly in his face he can do something to either keep me at bay or send me flying, and if I go off the stage in an egg at high percent I'm usually not able to mash out in time to recover. I have to be so careful with my spacing in this matchup that I don't get a chance to apply any pressure of my own. I'm glad Yoshi's finally good in one of these games, but I feel like they might have gone a little too far. I dunno, he's a weird character to balance with his unorthodox moveset. He's either really good (this game) or really awful (every other game!).
Another one I really hate that's probably surprising is Charizard. I rarely fight him and I've only fought a couple of really good ones, but I was really caught off guard by how many tools he has that make it hard for me to get in on him. Multiple jumps makes him hard to reach, fire breath that gimps me more often than not, rock smash has armor that can make it difficult to approach, he's pretty heavy so he's not easy to kill, it's just really awkward to fight him. Bowser is difficult for similar reasons, except he has a much easier time gimping me (if he jumps at me and side b's me while I'm trying to recover there's literally nothing I can do, I have to commit to either a dodge or a counter and he can punish me if I'm wrong).
Other match-ups I don't like are Falcon and Sheik. I feel like we're playing similar characters since we both have really great speed and hit hard, but their aerials are 10x better than mine so they have a lot more options for approaching, retreating, and recovery, so I'm left trying to make a read with my counter or armor but usually get wrecked pretty bad since I have so many less options. And of course, any Mario/Dr. Mario that knows about the cape to interrupt jolt haymaker trick is almost unwinnable. I still don't know how to deal with that, I just have to try and delay my special until the last second possible and hope they mistime it so I can counter instead.
I've heard lots of Little Mac mains whine about Rosalina but I don't actually hate it too much, it's probably in her advantage but I can usually knock the Luma off the stage with just a couple of hits and she's pretty predictable on her own. I was also very scared of Kirby and Jigglypuff at first since they're so great in the air but I was surprised to see that I win really often against these characters since they die at such early percentages.