How's that work out though? See, the thing abou the N64 compared to modern games (and game controllers) was that the Analog stick and the Digital Pad were never secondary to each other. It was either one or the other.
A game like Mario 64 uses the analog stick and the Z Button, but the L button and D-Pad are never once used (or functional) for the game. Thus, you'd hold the controller with the middle and right prongs.
Kirby 64, meanwhile, uses Digital pad exclusively. The shoulder buttons don't get any real use, and Z is flat out ignored. You hold it on the right and left prongs when you play.
It's understandble, really, they went this way: Analog control and full 3D movement were fledgling at the time, so it makes sense you'd design your game to work around one form of control. It's partially why the PSX with analog, the PS2, and the PS3 controllers all are a little odd: In an era where analog control is the focus, they have their left analog stick in a "secondary" position, which is a little counter-intuitive.