Since the N64, they've been the worst.

Since the DS, not including the 3DS XL, they've made the worst ergonomical handhelds as well. Since the DS Lite, also not including the 3DS XL, their portables also have a certain cheapness about them. Flimsy controls on the DS Lite/DSi, crappy Start/Select on the regular 3DS, the complaints of the original 3DS top screen being scratched when closing the 3DS.

N64 was the best controller ever.
Xbox controllers are ok, and I don't really like playstation controllers.

That first example of what you call a D-pad is incorrect, 4 buttons in a cross shape doesn't equal the design functionality of a cross that would go on to be the basis for most modern consoles controls.

However, I do agree with to an extent with you thoughts, Nintendo doesn't always create their innovations but there is no doubt they make them viable if not perfect the innovations they bring to the console industry.

- To this day most traditional controllers still are based on the design of the SNES/Super Famicom.

- There is no doubt that Nintendo's adoption during the N64 era of Analog control and Force feedback pushed the industry into making those features standard.

- There were wrieless controller before but the Wavebird on the GC clearly became the standard by which all first and most quality 3rd party wireless controllers would be judged against.

- Motion controls existed before the Wii (even on a few Nintendo handhelds) but no doubt the Wii forced the issue, although I think we can all concede the Kinetic was a truely impressive and near perfect counter blow by Microsoft.

Really aside from dual analog sticks, unless one would consider the Virtual Boy's dual D-Pads as the origin which I don't, most major console controller shifts and features usually originate or are mastered by Nintendo controllers first. So yeah, they have helped make some of the best controllers, although the fact is most of their innovations and big moves were years ago and I think them cheaping out on the Wii U's Gamepad has kept them from being at the head of another potential movement in game controllers.

Damn, am I the only person who likes motion gaming and the wiimote in the world? I was quite disappointed when I found out the Wii U would have a gamepad in contrast. Anyway, I didn't like the N64 controller, it was too bulky. Other than that, I like most of Nintendo's controller.

It all depends what you're a fanboy of.

The Wii-U tablet and the Pro controller are some of the most comfortable controllers I've used. I didn't think it was possible to get more comfortable for me than the 360 controller. The PS3 controller is awful for my hands and in my opinion feels cheaper out of the rest. In the end though like many things video game wise it comes down to personal opinion. Nobody has the same sized/shaped hands and each controller will handle differently for each person.

I thought some of Nintendo controllers were pretty good.

NES still my classic fav controller.

Not at all. I tend to prefer Nintnedo consoles and last gen I found the 360 controller design the most comfortable I had ever use. This gen the Wii-U controllers are the most comfortable for me. The Pro controller doesn't differ in shape from the 360 controller much and the analog placement is comfortable for me.  I just wish the analog sticks were concave like the 360s. 

You are not.. it fit perfect in my hand when I played games with the analog stick

The D-Pad on the other hand was horrible

Gamecube was their best effort, followed by SNES and NES. 64 and Wii I was never crazy about, but dealt with them.

While Sony barely deviates keeping me happy and comfortable Nintendo swings wildly back and forth innovating with mixed results. So, hard to say. I am a creature of habit so I am happy to find a good design like the dual shock and stick with it with minor deviations.