The N64 controller was actually quite ingenious, but its genius was never utilized. I imagine that it had three prongs so that developers could choose between making a 3D game for the analogue stick (middle of the controller) or a 2D game for the D-pad (left side of the controller). The N64 controller essentially has an SNES controller built into it. Sadly, developers seldom if ever utilized this; I've played a total of one N64 game that used the D-pad.
This does, however, bode well for a potential N64 Classic. If Nintendo itself doesn't take advantage of this to put games from the 8- and 16-bit eras on the system, then modders will, and we'll never have to swap out controllers in order to use a solid D-pad.
Edited by Geoffrey, 10 November 2017 - 06:26 PM.