I'm not sure why you'd site the 64 as an example of good controls. AFAIC it's one of the worst controllers in video game history.
The N64 was Nintendo's 1st foray into 3D gaming and they correctly designed their controller so it was possible for the player to move the camera and their avatar at the same time and independently of each other. The C stick was added to the GC controller, on the opposite side of the joystick, so once again, player's could easily operate them simultaneously. There is no C stick on the wiimote/nunchuk, but once again, there is a D-pad and joystick designed to be operated simultaneously. It boggles the mind as to why Nintendo left the joystick and D-pad to be only accessible one at a time on the 3DS.
On another note, the N64 controller is far from one of the worst controllers in video game history. The very left most side was useless, but it was probably one of the most ergonomic controllers ever designed.