Corneria looks dated graphically. The backgrounds are sparse and you can tell it's from a launch window Gamecube game. I'd like to see them update the stage both in terms of graphics and using the knowledge of what worked and didn't work in the past. The latter is far more interesting to me though.
I've read about people absolutely hating Jungle Japes. While I still think it holds up graphically on 3DS' low resolution screen (and with the backgrounds being mostly shadow), I can see where people have a problem with it. The side platforms are too small and due to the raging water and that f-ing claptrap, you spend a lot of time fighting the stage than other players. Also, I'm not a terribly big fan of stages set at dusk (the main reason I dock points from Bridge of Eldin in Brawl). I find it harder to follow the action.
Mushroomy Kingdom strips that level from Super Mario Bros. of all of its charm. They turned one of the most iconic first levels in video games into a boring desert. If they really wanted to go the whole abandoned-level-is-abandoned route, I feel like there were better ways to do it. Maybe include some new platforms, giant mushrooms and vines, or some cameos from Mario characters who have been MIA for years hiding out there because they're sick of that mofo defeating them (e.g. Mouser, Tryclyde from Super Mario Bros. 2), all that while keeping the aesthetics of the original stage instead of one that looks nothing like it. They could have had a lot more fun with it than they did.
Golden Plains is okay, but they probably thought the hook (e.g. turn gold, get a minor stat boost for a few seconds or so) was cooler than it ended up being. It's one of my least favorite stages in the game, but I don't hate playing on it. Dreamland/Gameboy is alright but a missed opportunity. I think it would have been better if it switched between different Gameboy games as in it'd simultaneously been a pea soup green Gameboy stage for Mario, Kirby, Zelda, Mega Mam, Donkey Kong, Metroid, and Pac-Man, switching randomly between those themes.