Blaming 3D for the quality of Munch's Oddysee is like blaming the inclusion of Munch and Vykkerz Labz. It wasn't the addition of new things, but the lack of the old values.
It must be said, though, that 3D programming and mechanics are much more complex than 2D mechanics, by at least one order of magnitude. A 3D game needs many more resources devoted to that side of development rather than design. But using that as a mark against it is equivalent to saying "2D games are better than 3D because they're easier to make."
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