Well it wouldn't be a strike against it, but yeah that's been a common theory for both Magicant and Mute City because A: they're both excellent stages, B: they're suspiciously not handheld-based, C: it would be crazy to have a unique stage in both versions for F-Zero and Mother when Metroid, StarFox, DK, Wario and Yoshi can't even get that, and D: up-porting stages from the 3DS to Wii U is likely much easier than vice versa so there's no real reason to not have new F-Zero or Mother stages when perfectly good ones already exist on 3DS and aren't handheld specific so they wouldn't be out of place on Wii U.
For those reasons, I'm about 95% sure that the Wii U version will have HD Magicant and Mute City, maybe with some slight changes.