An iteresting fact about Cartoons.
The more simplified something get's the more iconic it becomes. Because Toon Link is more cartoonish than a realistic looking Link, Toon Link's simple design is more recognizable and distinguishable. This is in the more general sense because those of us who play the games have a different understanding, however the average individual would find Toon Link's design more impressionable.
Scott McCloud talks a lot about this
Of course there is more about it and he goes into depth.
Well, let's start with the basic question regarding who is the more iconic Link. Uncanny valley. A realistic-looking Link will stand out far more with his odd clothes and behavior than a cartoon version of him, where these oddities are the norm.
A lot of people regard OoT as being the best Zelda game to date. Also, Windwaker really had no hype on release because everybody was expecting another OoT/Majora's Mask type game. I'm going to just assume that anybody who has played Windwaker has indeed already played OoT.
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"... when you look at a photo or realistic drawing of a face, you see it as the face of another. But when you enter the world of the cartoon, you see yourself."
The way we view ourselves is not realistic at all. However the way we view others is realistic.
If I watch TV and see a person there, I won't assume the person is tiny and inside the actual box. That is not realistic. Therefore, the way we view others (via TV in this case) is most certainly not realistic.