Some that immediately jump to mind for me: Arms, Pokken Tournament, The Legend of Zelda: Windwaker (for home console… so Spirit Tracks doesn’t count!), Pokémon Let’s Go Pikachu/Eevee, Super Mario Sunshine.

(Here’s a concept for my dream Zelda game: Windwaker art style but without all the ocean travel. Give the game a more dire atmosphere, somewhat along the lines of Majora’s Mask, fill it with dungeons that are just as good as in traditional 3D Zelda, and make it as wide and open as Tears of the Kingdom.)

F-Zero GX; bring the series back to life with the same rock 'n' roll attitude and blistering speed, but with the chaos and insanity possible on modern hardware.

The Last Story; the first game was an excellent starting point that could really shine today with less limited hardware.

Astral Chain

Do Kyle Hyde games (Hotel Dusk, Last Window) count? They own the IP but didn't develop them, so assume they do. Anyway, we need more Kyle Hyde.

Ocarina of Time / Majora's Mask
A Link to the Past
F-Zero GX
Star Fox Adventures <3
Star Fox 64
Super Mario 64
Super Mario Bros. 3
Super Mario Sunshine
Metroid Prime 1+2 (as in, the same world design and progression, which 3+4 didn't have)

First of all, @bold: that sounds amazing :)

Second of all, I hadn't really thought about this question before. Usually I want a sequel to continue a story line, but since Nintendo typically treats narrative as a secondary or even tertiary concern, I don't often think of the company when pondering follow-ups.

Golden Sun: Dark Dawn needs some closure. Same for Kid Icarus: Uprising. Metroid Prime 4 needs a sequel post haste, to demonstrate the sub-series still has a future and help disgruntled fans move on.

Star Fox Adventures! That’s a good one, completely slipped my mind. Yeah definitely would love to see a sequel to that one. Also to an extent I would argue Mario Sunshine is a sequel to 64 in all but name. It does pretty much everything 64 did but with some new gameplay ideas e.g. FLUDD.

Excitebike 64
Kirby’s Dream Course

Captain Toad Treasure Tracker!!

Kid Icarus, the NES game!