I disagree with many you listed, as Twilight Princess, Smash Bros. Brawl, StarFox Adventures, Metroid Prime 2, and Super Paper Mario are all games I really like (especially TP and Brawl as they're in my top 10 of all time), but the one I will 100% agree with is Other M. Admittedly, I was kind of skeptical of it before release already, but it still ended up being pretty disappointing, and easily one of the worst in the series.

Others worth mentioning to me are Paper Mario: Sticker Star, Kirby's Return to Dreamland, Spirit Tracks, Tri Force Heroes, Hyrule Warriors and StarFox Assault.

Paper Mario sticker star and NSMB2 are the top that stand out.

Pokemon Battle revolution
mario party 8
Fates (while not bad, did not live up to awakening imo, but rightfully so)
kirby triple deluxe, to regular compared (planet robobot is amazing though)

BUT THE ABSOLUTE MOST DISAPPOINTING NINTENDO GAME is........Pokemon Sun & Moon

The OP list (specifically Metroid Prime 2 and FE Fates) triggers me, but setting that aside...

Other M, Skyward Sword, Star Fox Adventures, Star Fox Zero, most recent Mario RPGs, New Super Mario Bros, and Xenoblade X all come to mind.

Here's my list:

Wind Waker - I liked the art style but the flooded world felt very boring to me.

Twilight Princess - The dungeons in this game were quite good. Though to be honest the hype and speculations surrounding this game's world made me have expectations that were not really fulfilled until BoTW came out. The motion control hype around this game for Wii made me have expectations that were not fulfilled until Skyward Sword.

Super Mario 3D Land - It is a competent platformer that takes the worst of 2D Mario and brings it to 3D.

Super Mario 3D World - Similar gripes to 3D Land but better thanks to level variety and co-op. Oddly enough I want a DX version for Switch because it is still a good game (just not on the same level as Odyssey, Galaxy/Galaxy 2, Sunshine for me)

Super Mario 64 - This is by far the most controversial choice. I tried playing this game after Sunshine and the controls just felt off.

Super Mario 64 DS - The game itself is not at fault as much as the DS is for lacking an analog thumbstick.

Star Fox Zero - The gameplay barely evolved from Star Fox 64, the graphics were awful (which I would not have cared about much if the game was good), the motion controls were way too complex. It had been years since we got a new Star Fox and this was major let down.

Piling on the Metroid: Other M crowd here.

Star Fox Adventures is a great game. I hope it gets a Switch remaster to piss you all off.

Pretty much every Yoshi's Island game after the SNES one. Yoshi's Island DS was basically the equivalent of the Japanese Super Mario Bros 2, in the sense that it had some of the most difficult, frustrating level design I've ever seen in a Nintendo game, often due to fake difficulty. Just beating the game on its own without 100% is a nightmare.

So what do they do to fix this in Yoshi's New Island? Literally turn it into a game for babies by dumbing it down to all hell. The levels offer pretty much no challenge whatsoever, the soundtrack is generic at best (and ear-bleeding at worst), and I didn't even feel motivated to try for 100%. If YIDS is like Lost Levels, this game is like NSMB2.

As for Yoshi's Woolly World, all my desire to play that was immediately killed by the Double Yoshi Exploshi commercial. I may pick it up one day, but not unless it's vastly different from what I got from the advertising. Feels like this series has finally found its true calling: Something exclusively for little kids.

I really like Metroid Other M, but a lot of people seem to dislike it.

For me the most disappointing Nintendo games have to be:
Star fox Adventures.
Super Mario Sunshine

As the Xeno series is my favorite series, XC2 was far from the evolution it should have been. Easily my most disappointed game by a LOOOOOOOONG shot.

I would need to say Zelda Twilight Princes, Zelda OoT is still my best game ever, and Zelda TP was next 3D Zelda that I will play after OoT and I had huge expectations, and I was disappointment. It was still good game, but IMO noticeably worse than OoT and probably my least favorite 3D Zelda.

Second one would probably be DK64, also had huge expectations after Mario 64 and Banjo Kazooie, but DK64 was not nearly good game like those.