It actually would be neat if, similar to the Oracle titles on the Gameboy, there were two Zelda games in development for the Gamecube together. The first would be the internally developed and already announced Wind Waker sequel with young Link and cel-shaded graphics and the second would be a more realistic (but not TOO realistic - think Lord of the Ring movies) Zelda game from Capcom/Mikami featuring adult Link. The second would of course, be sort of a continuation of the first and aimed at the teen/adult audience while the first would be for all ages like all the previous Zelda games.
I'd actually really like to see that. I LOVED the cel-shaded style of Wind Waker and wouldn't mind (in fact, I'd prefer) if it became the standard style of Nintendo's future Zelda games but, on the other hand, it would be interesting to see a darker more mature spin of the series. It wouldn't have tons of gore or anything. It would just be A LOT more intense, violent, and scary which is why Mikami would be PERFECT for it.
There'd only be two BIG problems. Nintendo's Zelda game would be unfairly labeled the "one for kids" and, worst of all, it would APPEAR as if Nintendo was giving in to all the idiots who refused to like/play Wind Waker just because of the cel-shaded graphics. I can already hear them gloating about how "Nintendo learned from its mistake and is finally getting a clue". Bastards!
So, actually, this probably isn't a good idea and I concur that an original game with franchise potential would be better.