The Legend of Zelda: The Minish Cap:

Wasting an entire button on a poor replacement for proper sidequest design. So instead of doing sidequests, you find stones throughout the world that you can "fuse" with other people, which unlocks things in the world. Some of these things require a secondary or third unlock.

Secret of Mana: Any charge past the second level is practically worthless. To fully contextualize; Mana is an action RPG where you have an attack charge meter. Spam it, and your damage hits the floor.

Sim Earth: Surprisingly, a lack of data. There was only so much they could present for the timing of the game vs the constraints of the simulation.

Final Fantasy 5: Unskipable cutscenes. This is a problem in the series in general (from 4 onward), but I'm singling this one out because it's my favorite in the series. (Worth noting that the pacing isn't even; there are parts with a lot of cutscenes, with the early part of the final world being probably the worst section, but there's that 7 minute cutscene (judging from a speedrun) near the end of the first world.)

Skyrim: They got rid of spellmaking in this installment.

Earlier TES games: Stat growth is handled poorly. In Arena and Daggerfall, it's RNG; in Morrowind and Oblivion, the timing of when you raise certain skills matters when it shouldn't. It doesn't help that HP gain from Endurance is not retroactive, so if you want high HP in the long run, you have to raise Endurance first.

Wizardry 8: Combat tends to drag on. Also, what is probably the hardest part of the game, the first time through Arnika Road, is far too early in the game. (The hardest part of the game should really be at/near the end, not early on when the player is still trying to get their bearings and hasn't acquired the neat high level abilities yet.)

Final Fantasy Adventure: The fact that HP and MP recover fully when you level up, which feels unnatural (it makes the precise timing of level ups too important) and trivializes resource management (for a (nearly) pure mage setup, I find that I level up before my MP runs low enough to need an Ether).

Oooh, Lies and damned statistics is a good pet peeve.

As to the Fallout example, that is indeed a problem of many games. 99 potions and the only reason you sold them is because they have high potions in stock.

Impossible Boss
Death's Door,
Greak: Memories of Azur,
Tunic

"Impossible Bonus Level" or "Time Trials" as some kind of reward
Steamworld Dig 2,
Owlboy
several Tomb Raider games

Backtracking
Anachronox
Knights of the old Republic

Ending to the Story not satisfying, or no Ending at all / cliffhanger
Eastward
Anachronox,
Runaway 2
The Book of Unwritten Tales 2

Story/Character is retroactively ruined in a future instalment of the series
The Longest Journey

It's not on GOG
Oceanhorn 2
Uncharted: Lost Legacy
Stray
Return to Monkey Island

It's not out yet
Sea of Stars

I'm not sure if I'd call it my "favorite game", but as I am currently playing Star Wars Dark Forces 2: Jedi Knight, I dislike how in many levels, if you find out at the end of the level that you didn't find all the secrets, you can't necessarily backtrack to earlier parts of the levels, to try to find the missing secrets.

There are many parts where you have to e.g. drop down somewhere, and there is no way to get back up, so all the earlier parts of the level become inaccessible then. I try to cope with this by:

a) Doing a special save if I recognize a point of no return (so I can load that savepoint again, if I need to go backwards).

b) Watching beforehand Youtube videos of the DF2 secrets in the level I am supposed to play, so that I will not miss them. I hate doing this, it is like playing an adventure game with a walkthrough, but then what can I do?

"Why do you need to find all the secrets anyway? Can't you just keep playing without finding all the secrets?".

Well, I guess normally I could, but DF2 has this mechanic that you get extra "force skill stars" ONLY if you find all the secrets in the level. Miss one, and you don't get the extra stars.

Plus, sometimes the secrets are really beneficial, like getting some powerful weapon early. Did you defeat all the Weapons (in FF7)? Yeah I know they are optional, but still.

At least I had to carefully follow a FAQ/Walkthrough in order to beat the Ruby Weapon, I think. A very finely tuned plan what kind of skillset you must have by the time you decide to fight it, what to do when etc. I think there were even some gimmicky things that you had to kill one (or more?) of your own team members during the fight as that somehow oddly helped you in defeating the Weapon boss...

I don't recall how hard or easy FF8 was, I just remember being bored to tears by pulling spells from enemies during fights, and the whole story of the game being quite incomprehensible to me, especially towards the end. So who was that black-haired chick again, and what was her relation to that older woman? Do I even care to find out?

Both FF7 and especially FF8 felt that they tried to make the story unnecessarily complicated. Well, maybe not FF7, but parts of the stories were gimmicky, and I prefer stories and atmosphere in earlier Final Fantasies, as well as Baldur's Gate 2 + expansion, Ultima Underworld etc.

I played Death's Door just a few weeks ago. Who was the impossible boss? I don't think I found any... or maybe my memory is bad, most likely.

For Ruby, I think I used a Mimic + KOTR strat that was popular at the time. But yeah, I mean overall. These games were meant for a new generation of JRPG players outside of Japan, so they went easy on the difficulty.

Yeah, FF8's plot becomes a terrible mess towards the end, and I preferred to believe the Squall is Dead theory until the writer denied it. I liked Kim Justice's retrospective, which also explains the story, convoluted as it is.

Problem is that:
* Only 2 of the weapons are actual challenges.
* Those 2 are single boss fights; they're not repeatable, and they're isolated. There's no challenge of going through a dungeon with dangerous random encounters in this game.
* The original Japanese release of the game didn't even have these 2 bosses.

Contrast this to Final Fantasy 5, where the game, as a whole, is a bit more of a challenge, not to mention the two superbosses being present in the original release of the game.

(FF5 also has the occasional superenemy that isn't a boss, appearing if you go into certain (avoidable) areas early in the game, and which can be an issue when it's first possible to encounter them; I think the only other FF game to do something like that is FF9 (Grand Dragons + Yams).) From my understanding, regarding FF8 (which I haven't played):
* The difficulty depends on how well you understand the system. If you know what you're doing and play optimally (that is, without self-imposed restrictions), the game is really easy, but if you don't understand the system, it's really hard. (FF2, which I have played, is like this as well.)
* If you boost your Magic stat (for example, by junctioning some spell to it), you'll draw more copies of a spell at a time, which should make drawing spells less boring.
* The best way to become powerful, to my understanding, is not to draw spells from enemies. Instead, get the Card Mod ability, turn enemies into cards, maybe play cards with people (this might not be necessary), then refine the cards (with the proper ability) into spells that you can then junction.
* Also, FF8 has level scaling. Remember how, with TES: Oblivion, enemy level scaling is a common complaint? Well, it happens here as well. And as a result, not that fun for veterans of the series (up to that point, and true even if you count only US releases).

Ever so many games: The minigames. Especially those that really push/require you to play them. Example: Horizon Forbidden West. You can't max the skill tree without the few XP gated behind playing the "chesslike" minigame.

So many jRPGs:
1 - After a while, combat becomes "hold attack to win" (or similar). Example: World of Final Fantasy.
2 - "Buy the guide" moments, like weird sidequests or cryptic mechanics. Final Fantasy 10-2's matchmaking and publicity.
3 - Surprise last boss. What is it with this genre and games pulling a last boss out of its digital butt that was unknown and not even hinted at before very close to the end. Example: Final Fantasy 8.
4 - Excessive late game/post game grind/superbosses. Example: Final Fantasy 12 and its hours-long fights and repeated fights to get random drops for that game's supergear.

Games with intentionally poor in-game help/mechanical obscurity/lack of in-game details: Example: Nioh 1, 2

Games that are so excessively balanced/"over polished" that they lose all charm or character. Example: Torchlight 1.

Games where the whole fun building experienced is ruined by specific, precise, requirements that largely prevent creativity in the building fun. Example: Zoo Tycoon.

Ever so many strategy games: You know the winner long before it actually ends. Example: Civilization 1-4 at least.

Reminds me of Chrono Trigger, where at one point there's a mandatory button mashing minigame. This is enough to make me not want to replay the game.

Or the insta-fail stealth sections in many games, including pretty much every Zelda from Ocarina of Time onward.

Would you rather have games that are balanced more like Morrowind?

Any game that tries to overbalance everything for multiplayer with no regard to single player/campaign balance or outright breaking stuff in it. Alternative would be keeping the SP and MP balance separate, but the only game I've seen do that so far is Starcraft 2.

Example - Battle for Middle Earth 1. The 1.3 patch screwed up the campaign so hard in numerous places it's not even funny. Can give specific examples if anyone's interested. Makes me extremely grateful that I have the box so I can patch my 1.0 version to 1.2 and ignore the later patch

Dragon's Dogma Dark Arisen

* Backtracking. Although I love Gransys, after the midpoint of the game -- where you have explored most of the larger areas of the map and night traversal is no longer as dangerous as at journey's start -- the amount of traversal and backtracking for fetch quests can sometimes become a monotonous chore... although I have played the game through 4+ times so it must not be that bad! Makes me wish the extreme amount of cut content (map) would have made it to release.

* Story. While I love the concepts in the story -- a rumination on what it means to be human -- the plotting has been butchered (IMO) for release. The first and last acts are strong, but the middle is uneven and sparse. DDDA had a difficult production and saw many large aspects that fleshed-out both the world and story cut just prior to release. Too bad.


Mafia II

* Things to do. While I tend to like the idea that the open world in Mafia II keeps the player channeled toward story, the limited nature of the world can over time magnify the artificiality of the world. Who has ever heard of a gangster world where you can't bet on horses, play cards, and get into general mischief? I sincerely wish there was more to do in this world. Mafia III suffered from the same... and a whole lot more.


God of War

* Sameness of enemies. There are very few things I can find to criticize about this game, but sameness of the enemies is one. While a few encounters were of a grand, spectacular scale, most were fights with modest humanoids (or similar).

The Witcher 1 has a great story but the controls are way too unorthodox.

While I don't know Morrowind (I've given it up quickly with a total lack of fun every time I've tried), what I mean is that the game shouldn't have super-symmetry or be balanced so every thing is effectively the (or very close to) same. There need to be some edges to find fun. Otherwise any choices you make are basically meaningless, too.