It's important to highlight that Nintendo have stayed true to one of their core principles: that the game should reflect the characteristics of the hardware it is played on. They've done this to great success before - think of Super Mario 64 pioneering 3d control with the analog stick, or the wiimote gestures used in Wii Sports.
They've correctly identified that mobile gaming is done with one hand, and even if this is not the first runner game on an iPhone, it's the right choice for a Mario game.
It would have been easy for them to whack up a virtual d-pad in a traditional 2d platform scroller, but I'm glad they've attempted something new.