I actually find the Wii U gamepad to be one of Nintendo's more comfortable controllers in recent years.
The 3DS isn't. All its buttons have these sharp edges, it's got this vestigial d-pad that I have to twist my thumb in weird ways to reach (or completely re-adjust how I hold the system).
I also really hated the Wiimote when held "NES Style." The d-pad is way, WAY too small on that thing, and not enough first-party games let you fall back to the Classic Controller Pro (which was even worse than the 3DS in the clicky/sticky buttons department)
I feel like Nintendo's biggest problem is ergonomics. They seem to like square, blocky things, but those aren't very comfortable to hold. The Wii U gamepad at least has grips on it, which is something I really wished the GBA SP, DS, and 3DS had.
We get it, okay. The Game & Watch was cool. But it's also, like, over 30 years old. Embrace change a little more, please.