Ocarina Of Time was great, but how many times can you play it? It's on the N64. It's twice on the GameCube; once on the Wind Waker pre-order disc, along with the Master Quest version, and then yet again on The Legend Of Zelda Collectors Edition disc. Okay, maybe not everyone pre-orders or subscribes to Nintendo Power to get these goodies, but still.
I guess there are other instruments used in Zelda games (like a flute, and I think there was another ocarina or flute in one of the GBC games) so it wouldn't be surprising if it showed up again, and I realize that it was really just an example...but a microphone on the controller may be of limited use and it's crowded enough as it is.
Okay, maybe not too-limited use...the DS uses it in some games, there's always online chat, Hey You Pikachu!, Mario Party 6, Mario Party 7, Odama, and other crazy uses Nintendo could come up with but I think a headset would be more comfortable (not to mention more stylish, and, you know, "hardcore"-looking. Maybe).