While it's obvious the N64 controller was designed for either D-pad or anolog use, it was made quickly obsolete my controllers that let you use both
I wouldn't say "quickly," the DualShock didn't come to the US until 2 years after the N64 did.
IMHO, Sony's Dual Analog/DualShock is about as good as gamepads come, which is probably why it's remained almost unchanged for 3 generations of consoles now.
Which is funny, the main reason I hated the PS2 and hate the PS3 is the controller. The design is what, 13 years old now? It's so uncomfortable. The trigger buttons suck, the analog stick placement sucks (placed where they fit, not where they belong), the general feel sucks. The 360 controller has the main stick moved to a more comfortable location, better triggers, and is sculpted to better fit your hand.
I can't fathom why anyone would prefer a 13 year old design.