Skyward Sword was not cell-shaded. It just had a highly stylized design aesthetic.

In general less realistic, more stylized designs hold up better over time. A game like Grim Fandago still holds up wonderfully compared to the other 3D games of its time.

But I would say cell-shading is a blight in most cases.

Cell-shading is a technique used most often to add black lines around models in an attempt to give them an almost hand drawn look. It's really ugly most of the time.

The only game I can think of that I really liked it in was Jet Set Radio.