Based on those five franchises, I would say...
Super Mario - 3D. I'd choose Odyssey and Bowser's Fury over Wonder. That's not a knock on Wonder; it's just that 3D Mario is on another level.
The Legend of Zelda - 3D. This is fairly easy. BotW and TotK are two of the best games ever made. Echoes of Wisdom is good, not great.
Donkey Kong - 2D. I loved my time with Bananza. Right now it's my GOTY. But Tropical Freeze (if that's truly "modern day") wins.
Metroid - 2D. This is, of course, a guess, since we don't know how MP4 will turn out. But it will be tough to top Dread.
Kirby - 3D. Kirby isn't really my favorite, 2D or 3D. But Forgotten Land tops recent 2D entries.
In general, I think that Nintendo has entered a second golden age during the Switch era, for both 2D and 3D games.
