It makes sense for the game to have optional Wii controls.
I mean it obviously has to have a traditional control scheme to be GCN compatible.
Additionally, the game wasn't designed with the Wii-mote in mind so I doubt it will be nearly as intuitive as in a game like Red Steel. Also unlike Red Steel which will likely use the sword-play sparingly, Zelda has very hack-n-slash style swordplay. Even my thumb has gotten exhausted pushing the button in some drawn out sword fights in Zelda titles over the years. Obviously full-on arm motions would not be an improvement in that regard and, for that matter, it could look sort of "wrong". The name is getting enough jokes as is.
I imagine a Zelda title built with the Wii-mote in mind will be very different than what we're used to in the series.
Instead of mercilessly hacking at enemies, it will be much more skill-based with an emphasis on using the sword to block attacks and executing a few well place stabs at "weak" spots which would be a huge improvement IMO. Zelda is supposed to be a thinking game but the sword fighting has moslty just been dumb button mashing.