Bayonetta: While the minigames work on your first playthrough, they do not when on repeated plays. This is a pain because the game's structured around replaying and bettering your scores.
Half-Minute Hero: While it loves to parody game conventions, it more than once leans into them a little too strongly, making it become the very thing it is trying to mock.
Link's Awakening: I really don't need the descriptions of power acorns every time, and I definitely don't need a warning that I can't pick up rocks or pots without the power bracelet every single time I accidentally touch one.
Castlevania: Aria of Sorrow: While I think it's easily the best game in the franchise, I do have to admit that a second screen that shows a persistent map adds a lot to the genre. Going from the later entries back to this one makes its absence immediately noticeable.
Metroid: Zero Mission: Zero Mission might be the most polished, best designed Metroid game out there, but I can't say it really adds a ton to the franchise. It's somewhat expected from a remake, but since Metroid games are already kind of samey, Zero Mission ends up feeling lacking in identity. The only parts it did contribute of its own, the Zero Suit mission, is a little too short and a stain on Samus' future characterisation.
Paper Mario: The Thousand-Year Door: It is the start of the series' fondness of trolling and wasting your time. Funny and cute at times, but when you're not in the mood for its bullshit, it just straight comes across as bad game design. Most of the locations are also kind of ugly and grimy, which is not an aesthetic direction I'm partial to.
Resident Evil 4: The game does a good job at switching between tones and plays out like a John Carpenter-esque romp, but this flow kind of breaks in the final chapters a bit. As soon as the game starts embracing the militarised enemies, the game often loses its charm to me.
Mega Man 2: Boss rush sections are never fun in any game. Sorry, Capcom. I know they're your jam, but to me they're tedious padding.
Undertale: Its art direction is all over the place, making it look like an amateur community project at times.
Final Fantasy IX: Most of the twists on the last two discs are a little clumsy and forced. It's mostly fine, but a noticeable step down from the impeccable first two discs.
Suikoden 2: Bad inventory system for a game with so many things to collect. Suikoden 2 has a bafflingly bad localisation for a game this amazing.
Metal Gear Solid 3: The game, like most of the series, will stop dead in its tracks to dump exposition in your lap. It's so strange that the game will go through such lengths to marry gameplay and story in some instances, and makes no attempts at all at other times. The only way to get a reasonable flow in your game is when you skip all the cutscenes, but that still leaves you with many treks that only exist to facilitate this ungraceful storytelling.
Final Fantasy VI: The game is a lot buggier than you probably realise. Entire features are hinted at and explained, but don't actually work. Luckily for the game, these tend to be under-the-hood, so it's easy to not be aware of them.
Pokémon Red/Blue: Same as FF6. Buggy, to the point where mechanics are hinted at which do not work. Since these bugs are not visible though, it's easy to miss them.