Imho, after NES and SNES controller ( 2 of the 3 controllers that set the industry standards), Nintendo dropped the ball badly.
Only switch pro controller 1/2 managed to delliver something good, not industry changing, but good.

Switch pro controller 2 is the best Nintendo controller, hands down.

I have a soft spot for the GameCube controller. It just feels so nice in my hands. It have some problems sure but the form factor - just how it is shaped, is my favorite on any controller. Many newer controllers feels heavy and/or bulky.

That said I probably think Wiimote + nunchuck is my favorite. I really like being able to position my hands in any position individually just mentioned in the thread before.
The Switch Joy Cons are not comfortable enough to hold unattached to the console. So even if they sort of have the same perk as the Wii setup it does not work as well.

Accidental diagonals, that's the problem. When you press up or down you'll register a diagonal input more often than not, which depending on the game can be a big problem. This is a very well documented and extended issue with both Pro Controllers.

I'm gonna throw in my vote for the Wiimote as well.

The separated design was great as it allowed me to hold my hands in a more comfortable and natural position, and playing games like Metroid Prime 3, Sin & Punishment Star Successor, RE4, or Red Steel 2 with it felt sublime.

Gamecube is the only factually correct answer. Fantastic ergonomics, bold design focused on gameplay. Many of Nintendo's controllers have regressed since - especially their standard controllers that have abandoned analog L/R. Sadly Nintendo abandoned Gamecube controller's tradition, and their contemporary controllers share more in common with the abomination that was the Classic Controller for the Wii. Switch Pro controllers are good, but not innovative in the least. Joycons are innovative, but also have poor ergonomics, and are somewhat inferior to the Wiimote in some ways (and somewhat superior in others). While Nintendo has maintained the idea of innovation in their controllers, this no longer extends to ergonomics and gameplay as it used to with the Gamecube. A Gamecube controller with slightly modernised ideas (e.g. separate L2/R2 without Z button; while maintaining the 'click' function of analog L/R), L3 and R3 in analog sticks, full size R analog, addition of select button, would have been the best possible design. Sadly, Nintendo moved away from this towards standardisation of their Pro controllers, resulting in a good, but hardly unique, controller.

I think there's too much "lets be cute for the sake of being cute" on the GameCube controller. 

The d-pad sucked and that was because they didn't even want to put the d-pad there to begin with, the Z trigger sucked again I don't think they intended for that to be on the pad. 

The diamond button layout of the Super Famicom is still the most sensible and logical for the widest variety of games. 

The Pro Controller 2 may be a bit bland, but it's super comfortable and super usable (barring Nintendo's aversion to analog triggers)

Just for shits n' giggles I tried using the re-released GameCube pad for some games of Mario Kart World just to see if it felt good to play a modern game with it ... that lasted for about 5 minutes before going back to the Pro Controller 2. 

Hear, hear. I agree the Switch 2 Pro Controller is tops. And I don't know if there's a better controller/game match than the GCN controller and Super Smash Bros. Melee. Those two are made for each other. They're almost symbiotic.

And that's the thing with the weirder Nintendo controllers. Many of them are perfect for certain games, but not ideal for every game.

Yeah Switch 2 Pro Controller would be my #2, it fits in my hands so comfortably, the buttons and sticks feel great, and the GR/GL buttons are a godsend as someone who hates "clicking the stick", I remapped R3/L3 to them and games that use them feel a million times better.

From someone who has been a Nintendo fan for about four decades now, there isn’t one controller that really stands out, but five of them I’d rank as great, and three as bad ideas or good ideas that needed a lot of work. If I had to pick one, Switch 2 Joycons, the most versatile and usable to date.

A+ tier: Switch 2 Joycons, SNES, Wii Remote.
A/A- tier: Switch 1 joycons, NES
C+ tier: N64
F tier: Wii U, and Gamecube.

A+ tier:
Switch 2 joycons with the magnetic attachment was a real game changer over the Switch 1. The biggest issue I had with Switch 1 was the rail wore out, meaning that if I even shook the console during play it would disconnect. Switch 2 eliminates that problem. Everything is better than Switch 1 with these. The mouse controls are also quite an interesting addition for games like Civ 7. These are a great second draft type of joy con, and I felt a lot better than the Wii Motion+ controllers, which added a half-baked gyroscope function… needless to say, after playing Cyberpunk 2077, the gyro controls in Switch 2 are a vast improvement.

SNES, the added L&R triggers and the diamond face buttons were not only a big improvement for the 16-but generation, but a standard set that lasts to present day. It’s not just Nintendo, but Sony’s PSX controllers are basically just a ripoff of the SNES controller… it’s OK, Nintendo ripped them off back with the L2/R2 triggers (which IMO were also a good addition).

Wii Remote, the most revolutionary controller in history; this was more or less the beginning of Nintendo’s multifaceted controller use and motion controls, including IR and accelerometer, later gyroscopic controls. It also helped shape the interface of Nintendo’s consoles and was instrumental in returning them to the top of the dedicated console industry. I’d also like to note that aesthetically, this was the first controller that actually looked nice since the SNES. I also feel that these controllers really captured the feel of the console in a way like no other console before it. So, while it is really the first-draft joy con, it’s an excellent first draft.

A tier:
Switch was the first controller Nintendo created that could be used ato convert the system from a home console into a handheld console. I might slip these into the A- tier because of the aforementioned rail issue. But, at the same time, that did occur after years of heavy use.

NES brought about the intuitive control scheme with the d-pad.

C+ tier:
N64, introduced the analog stick, but it would break easily. Not in the way of Switch drift, which could be fixed with some contact cleaner and a swirl, but they would literally break from wearing down, become loose, and required invasive repair methods that really only worked the one time (and they weren’t “good as new”, and later fixes didn’t really fix them). I went through a lot of controllers, but otherwise this did have the revolutionary analog feature… it’s just had that “prototype” quality to it since the obvious direction was to put the analog and d-pad on the same prong rather than two different prongs.

F tier:
Gamecube controller had the big greed button which blocked the tested and true diamond face button control method of the SNES. The triggers were springy. The D-pad was too small to use (like, even worse than the GBA). That Z-trigger was weirdly placed and tiny. And personally: the small size combined with how the controller kind of forces your hands to conform caused me hand cramps - to be fair, cramps were mainly caused by action games that required constant attention; games like Animal Crossing that allowed hand rest were a lot better. L

The Wii U was more a conceptual level failure, and I’m very glad Nintendo went back to the drawing board and went a different direction with the Switch. The whole screen on controller was a terrible idea to begin with, where tour’s have to split your attention. I get where they got the idea, the DS’s dual-screens… however, the DS was easy to have both screens in view; with the Wii U you’d have to hold it up in front of you to keep both screens in view. Also, the fact that there could be just one kind of defeated the purpose of having your own screen - and the whole asymmetrical gameplay was bullshit, just an excuse to cover the fact that only one controller could be used; it wasn’t optional, if you wanted to be player 2 you had to use a controller that didn’t have its own screen. Aesthetically, the bulky gamepad lacked the sleekness of the controllers of its predecessor or successor. Probably the thing that disappointed me most was the promise that you could play games anywhere in your house (really, I wanted to play it on a hammock outside during nice days); the reality was the range was barely more than the room the console was in.

I would have to put S1 joy cons as F tier, only because my kid's switch went through 3 pair via drift. I would chalk it up to kids, but i rarely played portable mode and had to buy a second set. S1 joy cons were just shit.