I’m going to go against the stream, and vote HD.
So, I’ll make it abundantly clear I’m speaking for myself because my opinion is far from what most fans think 😀
I didn’t really start to enjoy Nintendo’s 3D efforts until the Wii. Yeah, Super Mario 64 impressed me, so did Wave Race 64, but I found that wore off quickly. I found myself primarily playing SNES (as far as Nintendo games went) during the N64 era.
Rare, on the other hand: IMO they stole the show on the N64. But Nintendo lost them in the end.
I did enjoy Mario Kart 64 and Lylat Wars, more than the 2D era, but that was it. I didn’t really enjoy the Super Mario series in 3D until Galaxy, and Zelda didn’t happen until the HD era with Breath of the Wild.
On the downside of HD, Nintendo flubbed the Wii U. But not on the software side, what they needed was a great console for that software, and we got it with the Switch. During that generation they developed Xenoblade Chronicles X and Breath of the Wild, which remain two of my favourite games of all time. Mario Kart 8 Deluxe somehow became my most played Mario Kart game of all time on the Switch.
So, IMO, neither transition was perfect. But, speaking for myself, HD is a clear winner.
I describe myself as a little dose of toxic masculinity.