Skelux made a patch for sm64ds's controls like months ago, it plays nice with a analog stick and plays similar to the original 64 one.
Not giving you a link, but you could search for the rom and inject it onto a wii u vc one.
edit: nevermind, you were aware of the patch. There is also a prepatched rom, it plays fine with a analog stick or the 3ds circle pad (played it on a flashcard)