I do want to point out that if you install Crusade to a System-sensitive place, such as Program Files (the installer does this), then the controls will not be in the program folder, but in the VirtualStore folder in your home directory.
e.g.
C:\Users\TS Doqtor Kirby\AppData\Local\VirtualStore\Program Files\Super Smash Bros. Crusade\controls.ini
instead of
C:\Program Files\Super Smash Bros. Crusade\controls.ini