I have seen a lot of hate towards the original inverted-trident N64 controller which has always surprised me.  I always found it to be one of the best controllers that I have ever used.  Most of the dislike appears to be directed towards the analog stick which makes me think about the fact that I have always held the controller differently from how Nintendo recommends it be held and how basically all of my friends held it when I was growing up.

Have you ever tried the three finger approach to grasping the joystick of the N64 controller?  Use your thumb, index finger and middle finger of your left hand is used to clasp on to the joy-stick of the N64 controller.  Then use the thumb of your right hand to access the A, B, and C buttons, the index finger of your right hand to access the R button and the middle finger of your right hand to hit the Z-trigger.  It looks a bit weird and it's best if you rest the controller on your chest or lap while holding it this way as it doesn't provide for much upward support to hold the controller in the air.  That said, dedicating three whole fingers gives you amazing dexterity over the analog stick compared to just using a thumb.  Honestly, I started holding the controller this way when I first got the console as a kid back in 1996 and never went back.  I am not pretending to be an amazing gamer by any stretch, but I have never once felt that it was the N64 controller that was holding me back.  I find that analog stick to be great and amazingly responsive when it is held this way and it feels completely natural to use the middle finger of my right hand to access the Z trigger.  

Nintendo Recommended Holding Configuration for N64 Controller

Alternate (three finger on analog stick) method to grip N64 controller:

Back side for alternate grip:

Note that I am left-handed and so this may or may not have something to do with my affinity to hold the controller in this way... I have never seen anybody else hold the controller in this manner except for me.  That said, I wanted to share this alternate grip with the gaming community at large to see if it might be something that could help people to have a better experience with the N64 controller.  I recently started gaming on my N64 again as an adult and I really find that the N64's controller still holds up quite well to even modern controllers when I grip it in this unusual fashion.  I have absolutely no desire at all to try the modernized N64 controllers that more closely resemble the XBox controller as I am quite confident that I would have less control with such a controller compared to the classic inverted trident model pictured above.

You're bonkers! There is a special place in hell for people who control analog sticks with any other fingers than their thumbs.

Yeah, it looks weird but the fruits are the fruits.  Holding this controller this way has allowed me to beat competitive gamers at certain games on the N64.  I know this one guy who placed 3rd in a Dota tournament held in a city with over a million people, and I was able to beat him repeatedly in 1x1 Smash 64 matches using Ness as my main.  I basically cannot even get a KO against him in the later Smash games using the standard grip with the Gamecube controller and he kills me in basically every other game that I have ever played against him.

You can't use this type of grip with the Gamecube controller because it has a more standard type analog stick that needs to be moved further to get a response and the three fingers are just too slow: the thumb works way better.  That said, really slight movement of the N64 analog stick produces very effective responses and the three fingers helps to steady against over-movement or movement in a slightly wrong direction.  It's also a stiff analog stick that doesn't move all that easily (especially compared to the Gamecube controller) and so the three fingers allows you to apply a lot more force with less effort.  Finally, the surface area of the stick is really small and it is fairly slippery and so the three finger clasp allows you to change directions without having to move the position of your thumb and it gives you a good clamp on the stick that never slides off.  Also, because the stick is so small, the three finger hold feels really natural (the head of a modern analog stick is way too big for three fingers to feel comfortable).

I guess what I am saying is that the N64's analog stick is highly non-traditional and many say that it hasn't aged well.  That is why the Brawler64 controller that people recommend using today has the proper ball-style analog stick that is also found in the Gamecube controller.  My argument is that the N64 has a good analog stick but people should consider holding it in a non-standard manner to get peak performance out of it because of its weird design.  I would never recommend holding a Gamecube controller in this manner.

Usually with the N64 controller, the main complaints I hear are the analog stick due to the rough plastic material and the 3 handles. The stick is functional but rough to spin, so games that require to do full spins isn't the most comfortable, like Mario 64 against Bowser or the infamous Mario Party 1 minigames, overall it isn't the worst thing in the world but it can feel rough to go back to it compared to future control sticks, using it the standard way works fine for me. The 3 handles was always a stupid meme because games never require you to use every button, you just change your grip depending on the game, Mario 64 only requires center and right, Kirby 64 left and right grip, etc.

I just use one of these