Quick reminder, dissapointing does NOT mean BAD. NONE of these games are bad. To me these games just didn't live up to the immense hype and prestige they carried before release. Some are definitely better than others, some are even GOTY. They're all good from a technical standpoints but the HUGE fan inside me expected much better.

Quick example: The Force Awakens is entertaining as a stand alone movie so it's good but to me as a SW fan it was a dissapointing mess and i don't want to watch it ever again.

Feel free to dissagree and share your thoughts! 

Fire Emblem: Fates

Donkey Kong Country 3

Star Fox Adventures

Metroid Prime 2

Pokemon Colosseum

Super Paper Mario

Super Mario Sunshine

Metroid: Other M

Super Smash Bros: Brawl

Zelda: Twilight Princess

Wind Waker

Majora's Mask

Mario Sunshine

Starfox Adventures

Starfox Zero

Metroid Other M

All are not only disappointing but also legitimately bad games

Fire Emblem: Awakening, Mario Paper: Sticker Star, Super Mario 3D World and Animal Crossing: Let's go to the City come to mind.

Starfox Zero
Every pokémon game since B&W 2
MK7
NSMB2
Every Mario party since the 8

Disappointing in the sense of they were good franchises before or had good installments before but those ones suck.

Like I said some of these games are better than others but they aren't bad imo. TP is indeed not bad but to me it's just a wannabe OoT and MM clone and i did enjoy the game, but for being the most hyped Nintendo game of all time (along with SMB3) I sure felt let down as a huge Zelda fan. Same goes for the other games. 

Game and Wario
Star Fox Zero

Easy home runs but Nintendo shit the bed on these two. And for the record, I LOVE Star Fox Adventures.

I remember lots of Zelda fans being dissapointed in MM when it released and only strengthened OoT's reputation as GOAT.

Wind Waker was also despised for its kid graphics. I love them both! 

Yeah, to each their own. Hey, more power to ya, that 2 more games you can enjoy but I can't.

Coming after the amazing Ocarina I personally felt both dropped the ball, Majora cos the 3 day system was gimmicky and annoying, WW because the sailing was so goddamn boring and the art style retarded. IMHO of course.

I've never been disappointed by a Nintendo game before... until BotW that is. It's fine as a game by itself but I hate it as a Zelda game and what it means for the franchise. I'm not going to get into detail about it since I did that enough already, but it disappointed me enough to completely kill my interest in future 3D Zelda games. I'll still buy remakes and 2D Zeldas though (Unless they change the formula for those too).

I don't think I've ever been as disappointed by a game as with this one, the only thing that even comes close is the Beyond Good and Evil 2 announcement last year, that one legit ruined my day when I saw it.

mZuzek will probably scold me for mentioning the game and I'm sorry, but I had to say it, it's just that big of a disappointment to me.

Edit: Oh wait, Super Mario 3D Land was also pretty disappointing, but in a "meh" way. It's the blandest Mario game I've ever played, it feels like NSMB in 3D and that's it.

Xenoblade Chronicles X and Star Fox Zero.