This is PMBR. If they can't pull it off, no one can. It would be so epic to see him play like that - he'd be a really advanced character with the switching mechanism.
One question for thought: which part needs to be KO'd for it to count? Skull Kid or Majora?.
To balance, one of the two halves would either take priority (like Ice Climbers), or if either half dies they both die. It could go like this:
• Majora's Mask, separately controlled, would be faster and ungrounded completely. If Skull Kid dies, it would disappear. It'd be like leaving Popo and controlling Nana, only gaining total levitation. As Majora's Mask, you'd have far more control of the stage, but you'd also have to protect Skull Kid. Perhaps Skull Kid cannot be controlled without Majora's Mask, as he falls limp upon separation. The separation only allows control over the Mask, but if Skull Kid is destroyed, the Mask immediately disappears and you respawn with one less stock.
Wait a minute... Palutena would be a great addition! Another Kid Icarus rep with an available model. +1 Female, +1 Magic User. Has she been discussed?