The Bottom Line: This controller is maligned. Here's a revisionist view of it which argues that it is one of the most important controllers to come along.
The Nintendo 64 controller may be the most irony-loaded devices the world of video gaming has ever coughed up. It is universally loathed, ranking alongside the original "hamburger" controller which was bundled with the Xbox (and was quickly replaced by the smaller Controller S as the bundled controller and now doesn't exist anymore). But it was also responsible for many of the features you see today on standard controllers, including underneath finger triggers and the analog stick.
My relationship with Nintendo's controllers has been a love-hate one at best. When I was playing the NES, I didn't really think about the design too much because there was almost nothing to compare it to. But trying to pick it up and play it now can be a trial because the thing is small, boxy, and feels like it was made strictly for a child's hands (which it probably was). The Super NES controller is regarded as one of the greatest controllers ever created, but I hated it with with a passion that went unrivaled until I picked up the hamburger. It introduced shoulder buttons and always felt like an oversized plastic pill, which is what I've nicknamed it. Nintendo started getting right with the Nintendo 64 and the Gamecube, but then they took a great leap forward in technology with the Wii which was a small step back for yours truly. I love the Wii, but I have so much trouble handling the controller that I don't believe I can ever own one.
Now pay attention, because what I'm about to say next is extremely relevant to the way I look at video game controllers. I've probably mentioned my birth defect at various points during my long and storied Lunch career. But here is the full description: My right forearm is a mutation. I am missing close to half my forearm in general and probably over half of my actual hand. My pointer and pinky fingers for my right are among my mutant casualties. And my right wrist is almost immobile; I can move it off its fixed angle a few degrees, but it's not a natural movement and so it springs right back into place whenever I try to move it. My wrist keeps my hand permanently fixed at a 45 degree angle (more or less) sticking outward from my body. This makes doing certain simple things with my right hand a major pain.
With this in mind, the Nintendo 64 controller always felt like it was almost taylor-made for my hand. The buttons were always within reasonable reaching distance. The shoulder buttons still weren't worth any favors, but they were accessible. The unique grips and curves underneath the controller were always comfortable and easy to hold and so I never felt like I was going to strain my hand or get cramped up. Nintendo, with the Nintendo 64 controller, was clearly going for something more than a few buttons used to make video game characters do stuff with this one. Not only did they want to give you control, they wanted you to be comfortable at the helm.
There are two d-pads on the Nintendo 64 controller. Nintendo claimed they wanted to give you options, but most games for the console didn't let you use the actual d-pad. The "alternate" d-pad is the analog stick. Although it was hated at first, the d-pad proved to be a visionary control tool which offered an unprecedented amount of control in the 3D video games which would become the standard during this gaming evolutionary leap. A normal d-pad gives you four directions, and to go diagonally in a 3D platformer you would have to awkwardly try to hold two buttons on the d-pad. To go diagonally with the analog, you simply hold it in whatever direction you want to go in.
As to the left shoulder button which you also weren't using, well, I can't think of a way to finish that sentence. The clause there pretty much sums everything up. The whole left half of the Nintendo 64 controller is completely worthless for a large number of games. So what developers often did with the layout was put the left shoulder button function into the Z button, which is the small trigger on the controller's underside. It's an absurd layout to be sure, but you have to remember 3D gaming was brand new back then and so developers get a free pass because they weren't fully aware of just what they could do. Holding the middle prong just feels more natural anyway because the grip is more form-fitted than the other two grips, larger, and it makes pressing the Z button very natural and easy.
The action buttons on the right side of the controller are odd ducks. You have the A and B buttons, of course. But the C button is actually a cluster of small yellow buttons which basically form a third d-pad. They point in all four directions and functions are often allocated to them by referring to C up, C down, and so on. Nintendo's official statement was that the cluster would most commonly be used for the camera, but your chance of finding a game which uses them solely for camera control are about 50/50. It doesn't prove to be a problem as long as you can wire your head to use it correctly. (Nintendo just turned it into a full analog stick on the Gamecube controller.)
The standard Nintendo 64 controller is grey, but as has become normal for Big N, you can find it in whatever color you like rather easily. Probably the most unusal feature for the tri-pod controller is the memory card slot underneath, just north of the trigger. (Sega copied this for the Dreamcast controller.) I'm not sure why Nintendo decided to do this. Although long games which needed backup were getting very common by this time, the memory card slot doesn't really add anything to the controller. Attaching a rumble pack through the slot is nice but it doesn't have an important function. The main problem here is that the Nintendo 64 is a cartridge-based console and most of the games come equipped with a battery backup system of their very own, which renders memory cards pretty much useless.
I love this controller. It's very comfortable, which is all I ask. It performs its functions very handily despite the whole left side of the controller being useless. Many gamers hated Nintendo for introducing this. But Nintendo is having the last laugh after all that criticism. Today, we can't imagine playing video games without an analog stick, and trigger buttons are common. The Nintendo 64 controller turned out to be a prophecy.
N64 was a great console, yes it couldn't hold a candle to the PS1 which had better looking games, but nonetheless was a great console. But after all the years Ive played game on the thing I still don't understand this controller. Do I hold it in the middle or the sides, Do i play one handed? The hell Nintendo. As if my childhood wasn't confusing enough.