Yeah, I saw that episode of Game Theory. It's actually a pretty neat idea. - Then again, as a fan fiction writer, I like crazy fan-ficcy theories. I've also seen, (Cracked) the theory that MM represents the Stages of Grief and is basically Link's couch-trip after dealing with the loss of Navi and/or various other massive losses in his life after the Ocarina of Time ordeal. (He lost a lot there - his childhood, gained it back-but it's not the same, lost the illusion he had of immortality/realized he wasn't a Kokiri. He became a hero, then lost that Timeline and no one knows what he did. - The poor kid made a hell of a lot of sacrifices for Hyrule and is kind of alone on it all). It makes sense to me that he might have some kind of trip to deal with it all.
Hmm... maybe the whole thing was a coma-dream from when he got knocked off Epona and knocked out? He didn't actually wake up and chase the Skull Kid, he just had a long, weird dream that helped him work through some problems?
...
I think those are just idle theories, though. I think the canon is that "Link went to an actual alternate world called Termina and and saved it from an evil enchanted mask and a death-moon, then came home to Hyrule, grew up, had him some kids, and one of his grandsons/great-grandsons/down the line was a goatherd who became a werewolf."
So, "Link is Dead" in Majora's Mask? - Fun idea, a great one to play around with, but I don't see how it can be canon.