Nintendo did some innovations. Not all. The GC controller in many ways was a Nintendo take on what everyone else did at that time. The NES layout was one of many at the time, with others being similar, others having a d-pad just not with that shape, which was the smart part.
Nintendos breakthrough design was the SNES pad. Shoulder buttons and a layout that's used until today.
N64: Z-Trigger, added because you basically couldn't use both shoulder buttons with analog stick. And the famous analog stick. Which wans't the first one. Other than Sega and Sony though Nintendo was smart enough to go for analog right at the start. That is the big difference.
Adding further shoulder buttons, going dual analog and all that stuff, perfectioning a concept was done by others, Sony probably not the least.
Analog triggers are not Nintendo.
Tilt sensor or gyroscope, again not Nintendo. MS did that in the 90s.
Wiimote: Yeah, that was for the casual crowd. Though Sony had had Eyetoy before. Wiimote was better for some core games though, while being inferiour for many other coregames that use(d) classic contollers. Wiimote wasn't a bad idea, but it actually had many flaws depending on which kind of games one plays.
Now for handhelds:
Gameboy coied NES
Gameboy Advance is SNES minus X and Y
DS, though quite smart, basically took ideas from PDA's. Nintendo put that to good use, but if you know some old games for PDA's and handheld PC's you know where Nintendo took lots of inspiration. Other than that it's basically the SNES layout.
3DS: Adding a tilt sensor as standard, though not very Nintendo actually and analog, which Sony did first on the PSP. The Vita was a way fresher design contollerwise.

And finally, the Wii U gamepad. With a bit of bad will one could call it a Dual Shock 3 minus analog triggers plus touchscreen. Or you could say it's very inspired by the 3DS. In any case, Nintendo did an 'invention' for inventions sake, leading to them having no good use for a very long time except off tv.

Major breakthroughs:
D-Pad cross and basic layout: Made gaming with digital controls easier, more ergonomic (than others at that time)
Shoulder buttons and X-Y: More veratility, ergonomic breakthrough for additional buttons, ergonomic enhancement.
Analog stick as a standard: Great benefit for 3D games.

Second screen as touchscreen: Added a huge amount of versatility while keeping the mainscreen free for gaming. But that's primarily for Handheld gaming!

Not a total breakthrough:
Wiimote: casual controls by default.Sounds worse than it is. But the casual crowd has moved away and with many games motion control is inferior.

No breakthrough at all:
Innovation for innovations sake.
3D brought handhelds nowhere. Games did not benefit gameplaywise. So the good thing was you could turn it of.
And the Gamepad brought Wii U nowhere. The lack of proper usage for a far to long time is symptomatic. Now, there's a difference between gyro controls that could have worked with a standard controller and use of the second screen and touchscreen controls.

The SNES layout wa so great it was adopted by every major manufacturer and kept until today. That's a smart design. Looking at N64 and Gamcube controllers i'm not sure Nintendo ever understood how smart it was.

The N64 controller did not everything right. But Nintendo showed an understanding of what 3D games needed.

Now it's time for Nintendo to realize that new controllers don't neccessarily need to gameplay innovations and that some basic layouts are so good they just dont need replacement but maybe more subtle improvement

Maybe that's the reason why I always didn't like Nintendo's controllers.

As long as they don't make it something really wonky or difficult to have 3rd Party games, I wouldn't really mind

People complain too much about the controller. I can use whatever Nintendo throws at me without a problem.

I think people just suck at videogames and blame it on the controller! Just face it guys, you need to "git gud".

you're right,.. i can still remember that christmas when my mom gave me an snes and i marveled at the shoulder buttons for hours before even bothering to plug the system in. it was so foreign and new and innovative. i wonder if we'll ever get the full story about how nintendo came to the realization that adding more buttons would change everything.

nintendo never had a normale console

Am i the only one that didn't mind the N64 controller?

This is like saying the PS4 controller isn't a conventional controller because it has a touch pad on it.

The NES, SNES, N64, GameCube, have conventional controllers more or less, just because you introduce a new feature doesn't make a controller non conventional. Even the Wii U pad more or less is conventional, it just has a giant screen on it.

SNES was a "normal" controller for its time, just with a few extra buttons. So was the GC controller... only odd thing was the face button shapes on the right side. Dual analog sticks and analog shoulder buttons were already featured on previous controllers like the dual shock and the Dreamcast controller.

When people say they want a "normal" controller, that means they want something similar to the industry standard without being so radically different that it alters the fundamental way you play traditional games. The N64 and Wii controllers for example were made because you couldn't play 3D games or motion controlled games with the then industry-standard controllers. But you don't need a Wiimote or a touch screen to play the next COD, Madden, Fallout, GTA et.

The snes and gamecube were not revolutionary but other than that yes