Awful animation for characters' faces. Enough of the cast recycles their voice clips from Melee to bug me. The assist characters probably didn't have to look like they belonged on the Nintendo 64. And, so much of so many stages being recycled GameCube models and textures. That last one does bother me that much, yes.
It's debateable but Brawl does have a certain screwloose style of unpolished gameplay, with hilariously bad balance, a snail's pace, and dodging being so brokenly reliable that it completely stops any flow the game could have had... I denied it for a long while because I liked the new characters, but Brawl is kinda lame. Project M's tweaks do ultimately give it a more finished, less sloppy, somehow more professional feel, with the player having a significantly greater degree of control over their character. Although Sakurai has more or less said they don't give even a single crap about anything that sounds even a little competitive.
Basically, imagine, what if the effort put into Snake's Codec calls was applied to everything?