The transition from games being primarily 2D to primarily 3D in the 90s, and then later to HD were both significant shifts in how challenging games were to make. 3D required a whole new set of rules and norms, while HD and with it the shift to much more complex models, shaders, textures, etc was challenging for many developers.

Setting aside issues of hardware and commercial success for a moment and focusing just on the quality of the software itself, which do you think Nintendo pulled off better, their first generation of 3D games with the N64, or their first generation of HD games with Wii U?

3D definitely. Mario, Zelda, Donkey Kong, Star Fox etc. All the franchises they made into 3D seemed to work out really well.

They seemed to struggle more with HD with long waits between titles.

I don't see how any Wii U games changed the industry forever. In all fairness, Sony and Microsoft had already been making HD games for years by the time Nintendo started to.
Super Mario 64 and The Legend of Zelda: Ocarina of Time were groundbreaking. And of course, games like GoldenEye 007 were transformative as well.
3D easily wins.

Without question 3D. Mario 64 and Zelda OoT set the standard for 3D games and controls for 3D games. That's it. Just those 2 games alone crushes anything Nintendo did going to HD.

3D for me. For one, the jump to 3D is just a bigger, more consequential leap in general. For another, Nintendo absolutely crushed the transition to 3D. Its first attempt, Super Mario 64, remains one of the best, most revolutionary games of all time.

The company’s slow output on WiiU, meanwhile, suggests the demands of HD development were something of a struggle.

Definitely 3D. Nintendo struggled with HD development during the Wii U Era. The fact that their teams were still split between home console and handheld console development at the time didn't help things either. Nintendo made a smart move combining their teams together for the Switch.

They did a bad job in both cases. However, the transition to 3D was more disastrous for them. They basically handed Sony the video game market. While their 2D games set the market on fire and restored console gaming in the US.

The Wii U was kind of a disaster too, but it lead to the Switch which has awesome software.

Obviously 3D was infinitely better. I mean transitioning to 3D and HD aren't remotely comparable. Shift from 2D to 3D is a huge change and Nintendo absolutely nailed it, pretty much single handedly showing the entire industry how to do 3D games. N64's games simply blew everything else on the market away. While HD is just a matter of graphical fidelity increasing and so making assets and therefore games taking longer, but there is no gameplay shift from SD to HD.

Gotta vote 3D on this one.

*looks at SM64*

3d.