And actually I'd say Dark Samus is the bigger upgrade.
For sure, but it's an unfair one too. Going from an assist trophy to a proper character, it was always going to be a massive improvement since obviously assists won't be given as much care.
I also think Bowser looks ugly, by the way. People say it's because of the new lighting engine and while that might be true, Bowser's colors do look weird in every single shot he's in. It also doesn't look at all like a new model to me, just retextured from Smash 4.
Personally I'd say the biggest improvement was Zelda, but if redesigns don't count, then Zero Suit Samus.
She was an aberration, now she looks like an actual person.
Edit: oh and of course, cue "they nerfed boobs" hate. Oh, the internet.