Would love to see Spear Pillar return...maybe with Giratina replacing Cresselia and plunging the stage into the Distortion World? I get why some people hate Spear Pillar, but it's one of those incredibly iconic places that Sakurai tends to replace with stupid, irrelevant locations (Arena Ferox instead of Dragon's Table/Grima's Back, Windy Hill instead of Planet Wisp, Reset Bomb Forest instead of Lightning Chariot Base, Mario Circuit instead of Rainbow Road...I could go on for hours!) and we should be thankful we have an ACTUALLY IMPORTANT place from a game where the climax takes place!
Also, Sonic should get a returning stage...I mean, Green Hill's WAY too iconic to not be in the game, it's like leaving out Mushroom Kingdom. I personally think the Sonic franchise could also get a nice new stage on the Wii U version to represent the 'Modern Sonic' part of the series (Windy Hill doesn't). I'd choose City Escape or Rooftop Run for the Wii U and Planet Wisp for the 3DS.
A Bowser's Castle stage would be awesome, as would be a moving Rainbow Road with breathtaking scenarios! I'd also LOVE a Somnom Woods stage for the 3DS version, since Mario & Luigi Dream Team was a huge success and my personal handheld GOTY.