Among Nintendo's many franchises, 5 stand out as having recent releases in both 2D and 3D entries: Super Mario, The Legend of Zelda, Donkey Kong, Metroid, and Kirby.

Of course 2D mostly refers to the style of gameplay as they all pretty much use 3D graphics or 2.5D presentation as it were. Do you have a general preference for Nintendo's recent 2D or 3D output? I tend to think there is a bias towards 3D games because they are seen as more complex, ambitious, and more representative of the way we experience life. 

Are there some series you prefer in 2D but others in 3D?

Note, I'm only discussing contemporary Nintendo, not their classic 2D or 3D games.

Here are the most recent 2D and 3D entries for each franchise.

Mario:

3D - Super Mario Odyssey (or Bowser's Fury) 

vs.

2D - Super Mario Bros. Wonder

Zelda:

3D - The Legend of Zelda: Tears of the Kingdom

vs.

2D - The Legend of Zelda: Echoes of Wisdom (or Link's Awakening remake)

Donkey Kong:

3D - Donkey Kong Bananza

vs.

2D - Donkey Kong Country Tropical Freeze

Metroid:

3D - Metroid Prime 4: Beyond (upcoming)

vs.

2D - Metroid Dread

Kirby: 

3D - Kirby and the Forgotten Land

vs.

2D - Kirby Return to Dream Land (or Kirby Star Allies)

Mario 3D
Zelda 3D
Kirby 3D
DK 2D
Metroid 2D

Nintendo's peak 2D days ended with SNES, imo. And their peak 3D ended with N64. Not that they don't make great games still, they do. But I don't see the innovation that I saw during the N64 days anymore. Even Gamecube (for the most part; it had it moments, though) was a market step down.

But modern Nintendo is definitely at their best when making 3D games. Without a doubt.

Depends on the series. But also the era.

I used to be square in the 2D Mario camp prior to Galaxy, square in the 2D Zelda camp prior to Breath of the Wild. Still square in the 2D Metroid, Kirby, and Yoshi camp. For DK, I still prefer the DKC trilogy above classic DK and more modern DK. But post-DKC I do prefer the 3D games (especially if you include spiritual successors like Banjo Kazooie and Conker)… just nothing has grasped me the way DKC did in the 1990s. Kirby for me peaked in the same era with the Kirby Superstar Fun Pack.

For games like Kirby, DK, Smash Bros, and if you consider Pokémon to be Nintendo, then I’d say 2D. For games like Mario, Zelda, almost any Mario spinoff (MarioKart, Mario Tennis, etc.), and Metroid, then I’d say 3D.

For Mario I generally prefer the 3D games and prefer 3D World or Odyssey over Wonder. IDK why but Wonder just didn't resonate with me like it did with everyone else and I can't really explain why. 

For Zelda, Echoes of Wisdom is still on my shelf. But, I'm almost 100% positive based on previous entries I will like Tears of the Kingdom better. The only 2D Zelda game I've really liked is Link Between Worlds. I started with Ocarina of time and 2D just felt like a step back. 

For Kirby, I would generally say 2D but of the 2 more recent games I liked forgotten land way more. I just didn't like Star Allies all that much and thought it was one of the weaker 2D entries. Return to Dreamland is better, but still on the weaker side. Planet Robobot would be a harder choice. Still though, it's kind of an unfair comparison since Forgotten Lands has the novelty of being the first 3D game to its advantage. 

 For Metroid I've always preferred 3D. I'm terribly at navigation and adding a 3rd dimension doesn't help. Still love the prime series, but I think the formula works better in 2D. 

DK is similar to Kirby. Bananza has the advantage of being the first 3D DK game in a long time, and the first one with this style. Whereas Tropical Freeze as probably a better game overall, but didn't do that much different from DKCR so it didn't have the same impact. Overall I like 2D better, but like Bananza better than TF.

Perfection vs perfection. I prefer 3D Mario to 2D but 2D is incredible as well. Both forms of Zelda have some of the best games ever made in them. Donkey Kong I would say 2D but again 3D is fantastic. Metroid I like equally, and I've really only played the 3D Kirby so that one is 3D.

Both are among the very best in class for their respective genres.

I generally prefer 3D, though their 2D games like Mario Bros Wonder, Metroid Dread, Tropical Freeze, etc are also fantastic.

Now that we've had an experimental spinoff in Echoes of Wisdom, I'd love to see a traditional top down Zelda on Switch 2, that art style could really shine on it.

On the Switch the 2D game that really stood out was Metroid Dread. The rest of Nintendo's first party games that really stood out were all 3D. Of course most of the games they make are 3D, so it's a little unfair, but still, they definitely focus on 3D and it shows. I think Metroid Dread is the first 2D game in many years in which Nintendo was like hey let's make a badass 2D game that rivals anything else we make.

Which is fine. Indies pretty much dominate innovation in 2D gaming these days anyway.

It hurts to say this given how much of fan I am of the classic 2d Nintendo games but at this very moment the 3D games are better for Mario and Zelda. Wonder is a crappy 2d Mario (that wonder effect is so off putting) and EoW is so bad that it enrages me. Sad!