My favorite stage of all-time (in Smash 3DS) is Mute City. I love the feeling of traveling & the retro feel. Such a fun stage. I also have other favorites, like Paper Mario, Spirit Train, Gerudo Valley, Prism Tower, Magicant, Tortimer Island, Living Room, & Tomodachi Life.
3D Land, Golden Plains, Rainbow Road, Dreamland, Paper Mario, Prism Tower, Unova Pokemon League, Tortimer Island, Mute City, Tomodachi Life, Magicant (Or as I like to call it,"Dreamy Ice Cream Land") Living Room, and Pac-Maze
I love both the Paper Mario stage and Spirit Train. Even though the Bowser Castle in the Paper Mario stage can be a pain, the TTYD part makes up for it lol.