Wii remote + Nunchuk.

Comfortable to hold, lets me play with my hands further apart instead of scrunched together, good button feedback, IR pointer offers far superior aiming to an analogue stick, speaking of which the stick itself is still great for character movement and feels neither too stiff nor too loose, motion controls offer the potential for a greater degree of immersive connection and tactile satisfaction.

Probably my favourite console controller to date.

Gamecube. I mean, everything just felt so right. Smash Bros. Melee might or might not have something to do with how I feel about the controller. It had the right amount of buttons. The right shapes. It was just perfect.

Has to be the Gamecube controller. Perfect fit, responsive, satisfying button clicks and durable as hell.

Surprised there's so many Cubesters (GameCube hipsters) here.
The reality is the GameCube controller was garbage.

The d-pad was useless, the z-trigger was impossible to find, and the c-stick, X, and y buttons were awkward to use.

The L and R triggers were noisy, squishy, and unresponsive.

The face buttons were just all fucked up, the green one was gigantic, another was tiny, and the two grey ones were positioned in such a way that 2D fighters were terrible to play unless they were simplistic like Smash. It was so bad that Capcom had to cancel Street Fighter games because the controller was insufficient.

A lot of games were terrible with the GameCube controller, especially Virtual console games.

N64 for me, I loved the three-armed design, the Z trigger was perfectly placed and the joystick was really good (before it broke), d-pad was good and add-on's were cool and practical. It was also quite revolutionary and provided a proper means of playing true 3D games.

No other Nintendo controller comes close for me, the GC controller always seemed awkward to me, the Wii-mote was terrible and Wii U's Gamepad is the worst main controller ever conceived for a console, in my opinion.

GameCube controller is an automatic disqualification for me because the d-pad sucked so bad. Also the one Z-button was lame and the bean button layout was overrated, for regular fighters gimme a diamond shape anyday.

The Wii U game pad honestly I think is their best controller, it just looks stupid because it's so big and clunky but from a controller POV ... it even can to the aiming stuff the Wiimote does (see Splatoon). It's the most functional overall, good size d-pad, nice triggers, nice analogs, motion, the touchscreen stuff if you just look at it as a bonus is fine. The pad is so big that neither the d-pad or analog feel like they're in the "secondary" position. 

It's just too big (unneccessarily too IMO). They could've made the gamepad smaller and sleeker. 

Wii U Pro Controller is good too, but I don't like the d-pad and buttons being so close to each other.

Personally, I think the Gamecube as a whole is a thoroughly overrated console.
Sure, it was excellent hardware in terms of its power/size/price ratio, but coming after the N64, it was a big step down in software quality, in my opinion. So many franchises that were epic and boundary-pushing on N64 became lame and neutered on GCN.

I personally like the Gamecube controller.  I agree that the D-Pad is way too stiff (that said, the Game Boy and GBA D-Pads were just as bad) but apart from this gripe I find it to be an extremely comfortable controller.  One thing that I really appreciate about the GCN controller is that the A, B, X and Y buttons are all distinct shapes and sizes.  I find the Wii U gamepad really fustrating because it has 4 buttons that are shaped and feel exactly the same... Unless I am using the Gamepad regularly, I find myself constantly mixing up B, X and Y unless I look down at what I am doing.

I am not disagreeing with you but, in terms of RPGs, I thought that the Gamecube was a huge step up.  We're talking about games like: Skies of Arcadia, Paper Mario Thousand Year Door, Tales of Symphonia, Baten Kaitos, Fire Emblem Path of Radiance, a couple of really strong Harvest Moon games, etc...  I started playing RPGs a couple of years ago when I dusted off my Gamecube and I was blown away by just how many really stellar RPGs there are on this console.  The N64, Wii and Wii U came nowhere near the GCN in the RPG genre, in my opinion.

That said, In terms of mainline Mario games I have to agree with you.  I thought Sunshine was a massive let-down.

Gamecube except for the silly yellow C-stick which is easily replaced. Pro controller's analog sticks way too loose and slippery for me and the face buttons too low. N64 controllers C-buttons sucked and the analog stick wears out big time.

In terms of RPGs, fair enough, but seeing core franchises like Mario and Starfox go from being badass on 64 to lame on the Gamecube was a bitter pill to swallow.