slightly more Vocals for characters like Luigi, Wario, Snake, Sonic, Samus, Fox...
& more links to characters' homeworlds, like Mushroomy Kingdom would've been a great Subspace stage, and the Pleades would've been nice too...
...which would've landed on a Mario galaxy esque planet where you battle the Majora's Moon at the end, brought by a Primid wearing Majora's Mask sent by Gannondorf...