The reason that N64 controller had such an awkward ergonomic configuration was due to the analog stick it introduced. Nintendo was uncertain about the implementation of the stick, so they decided to meld two controllers into one. Their though process was:

-If the analog stick failed, developers would switch to D-pad centric games, and players would grasp the controller ala SNES style.

-If the analog stick succeeded, developers would make games that use the stick and players would merely ignore the left prong on the controller.

Unfortunately, despite the success of the analog stick, the d-pad and left shoulder button were still necessary for many developers. This left players awkwardly shifting between two different grasping positions.