Mine would have to be Ocarina of Time. OOT had a great storyline, and in my opinion, was the greatest game Miyomoto ever did. I didn't mind the cel-shading in TWW at all, i thought it was quite cute. But that's the thing, cel-shading is quite cute, while polygons are realistic. However, the graphics aren't the reason.
I got a different feel for the game OOT. I can't explain it. I love the game. Even though it was the average hero saves the princess story, this game brings that to the top. In The Wind Waker, i didn't get that same feeling. It felt like just another game even though it wasn't. OOT is special.
I'd prefer OOT's storyline over TWW, OOT's graphics, and its world. TWW's The Great Sea was too big for a ocean invested world. I just wonder if they made TWW set in Hyrule, it would be a much greater game, and it probably would outbeat OOT.