I guess i'll add to this:
Super Smash Bros. Melee - It ruined the amazing plot twist in Ocarina of Time for all eternity and Brawl followed up with the same. I played said game a few years after I played Melee and the plot twist was always in my head I was young at the time and I remember the walkthrough which was written straight after the game came out which said something along these lines: 'after you've finished the Spirit Temple, go to the Temple of Time for a sequence, you will guaranteed be suprised!'... . I know countless others have expressed the same annoyance. half of the characters in the game sucks ass too.
Zelda: Ocarina of Time - Water Temple sucks, the overworld also is way too barren, the child-adult mechanics isn't as fleshed out as it could have been, given that you only have to go back to child Link once after you've become adult. It could have also been used more for creative sidequests.
Zelda: Majora's Mask - After the amazing and long Anju-Kafei sidequest, you are unable to have obtained all the pieces of heart at that point because the mask you get from that sidequest is required to get one piece of heart earlier in the 3 day cycle meaning that if you wanna 100% complete the game and get the complete credits ending, you have to do the sidequest again.
Zelda: Wind Waker - A lot of the islands have nothing of interest on them. Windfall Island also being the only major city with any life to it was also sad.
Paper Mario: The Thousand-Year Door - General White's fetch quest. Other than that, I honestly can't think of anything really negative to say. An amazing experience from beginning to end which constantly does the little extra.
Undertale - Protagonist moves too slow, the puzzles are all also piss easy to the point they honestly shouldn't be there.
Cuphead - The sea captain boss. The only boss in the game you don't have to really learn attack patterns of and can instead just brute force your way to victory against. The music is also really appropriate for it's setting, but because of that, a lot of it feels really samey and unmemorable in sound.
Kid Icarus: Uprising - Stuck on a really outdated system which can make it hard to go back to it. Please re-release it on Switch!
Super Metroid - Progression can be really cryptic
Yoshi's Island - Sucks for completion 100%. Most of the levels have one or more points of no return, meaning you have to replay them a lot to access bonus levels.
Resident Evil 4 - The end parts are garbage. Who the fuck at Capcom thought it was a good idea to go full Michael Bay the last 2 hours?
Chibi-Robo - The game fails to make it clear what it's really about. What it feels like on the surface seems really boring, but the game is absolutely anything but once you get in to the meat of things.
Chrono Trigger - Crono should not have been a silent protagonist
Earthbound - The game has countless major flaws in the gameplay and inventory department, but the game managed to be incredible regardless.
Mother 3 - The locations are for the most part not anywhere near as exciting as the ones you find in Earthbound.
Super Mario Odyssey - Some of the worlds are lackluster in terms of content
Diddy Kong Racing - The courses designs are nothing much to write home about. They do their job, but not much more.
Banjo-Kazooie - The fall damage in unfair as hell and can often kill you and the flying controls + the attack are utter shit and almost singlehandedly ruins the final boss battle for me, the whole board game beforehand also really overstays it's welcome and that's something even the developers have admitted.
F-Zero GX - Some of the courses are an utter pain to get good at. The game also requires you to learn an unexplained advanced technique in order to properly enjoy it. It took me over 10 years to enjoy it properly due to that.
Phoenix Wright 1 - Case 5 which was added to the DS should have had more connetions to the original 4. Also, the game has some really annoying characters.
Phoenix Wright 3 - Same with the annoying characters. Case 5 also really jumped the shark in some areas.
Pokemon Black/White - The low health sound, sure it was great to remove it for the repetitive annoying added on sound, but I hate that they changed the song for it. That was a terrible idea. The only thing the new games after this have doen right is to remove that tune altogether (or you only hear the warning for a couple seconds).
