Hmmm...that's a good point. I hadn't thought about DKC and the games like it, but it was Rare that took the graphics as far as they did, utilizing SGI (Silicon Graphics) to make the game look 3D. In any case, you might be right about Link to the Past, could have just been Nintendo's idea to make it look cartoony. And for OoT and Majora's Mask, I see your point, but also, because the game looked more "realistic" than its predecessors, people wanted more and more.
The art style of Windwaker and it's sequels is unique, and I thought it was pretty neat. It's a shame that people didn't like that style, but it's their call I suppose. It's one of those risks that they decided to take, and it split the fan base, which is unfortunate.