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Id say that some 3D Sonic games like the Adventure Titles are good examples of pure platformers that take good advantage of the three dimensions (at least the Sonic & Shadow levels); it is of course worth noting that those games streamline things with the Home Attack
More villains need to be protagonists. BIS proves it can work. Ridley, Ganondorf, Fawful, Bowser, and Dimentio all for their own games!
In linear 3D platformers, the 3D is only a slight hindrance. Some level designs in 2D games, and the fast paced platforming of Donkey Kong Country: Tropical Freeze and Rayman Legends would be difficult to make, or impossible.
It's worse in open 3D platformers. They must be designed with backtracking in mind. Things like chase sequences or crumbling platforms are impossible. The platforming is usually very light. They tend to focus on exploration over platforming, too. This is why games like Super Mario 64 feel more like adventure games than true platformers.
Why is Super Mario Galaxy being mentioned? It's strengths are the same as 3D World's, the graphics, music, and creative level design. All of that is possible in a 2D game. Even Galaxy's gravity mechanic would work in 2D.