“I don’t think it’s because one game is better than the other. It’s just that compared to 2D, there seems to be more people who are not as comfortable with 3D controls. And maybe a wider range of people were more accepting of the New Super Mario Bros. series, which may have seemed simpler to them.” - NSMBU director, Masataka Takemoto

I also think it has a lot to do with people being uncomfortable with change. They are used to Mario in classic 2D style, so they don't have a high barrier for entry when tackling a new Mario game in that style. Throw things into 3D and people are too afraid to pick up a controller and try.