It's simply easier to navigate in only two directions (really primarily one -- go forward) in the 2D Mario games.
3D which allows one to go in any direction is more difficult. You can get lost for one.
It's the same reason Mario will always be more popular than Zelda ... it's far easier to play. People like straight forward action (running/jumping/stomping) over exploration based titles. Another reason why Metroid Prime with its emphasis on exploration will never be as popular as Call of Duty (blow everything up).
Though 3D World pretty much brings much of the experience of 2D Mario into 3D almost perfectly. It's probably too bad that 3D World is tethered to a dud of a console though. 3D World on the Wii probably would've sold 15-25million copies (more than either Galaxy game) with its multiplayer + tighter level design.
