The N64 controller is very comfortable.

And a few of you are viewing the controller as one single controller, which is of course understandable. However, the N64 controller is more like three different controllers in one. Most N64 games use the "left hand on the middle prong and right hand on the right prong" position. Some games use the "left hand on the left prong and right hand on the right prong" position. And the third position is "left hand on the left prong and right hand on the middle prong".

Only one position is ever meant to be used at a time. N64 game designers knew this and didn't require changing positions mid-game. Some buttons are inaccessible in each position and game designers took that into account.