A little while ago, I came across a modified SM64DS ROM (special thanks to Gimzie for sending me it) that fixes the game's flawed controls. I played through the game using this ROM, and let me tell you: It. Is. Amazing. It fixes many problems with the original controls, most notably the running situation (It makes it so that you don't need to hold a button to run), and adds some new stuff, such as all characters being able to wall-jump. I'd leave a download link, but the original file is a ROM, so I made an xdelta instead. Click here to download it. Also, you need a European ROM to use this patch.

(original source link removed because i just realized there's the ROM download there)