I considered making a thread like this though it was more general.
1. Any game without a "Restart from last checkpoint" option on the pause menu screen. Sometimes I know I screwed something up and I don't want to have to die just to restart where I was.
2. Any game with long cutscenes without a "Skip Cutscene" option as well as rewind, forward, and pause controls. This would be especially helpful on subsequent play-throughs.
3. Quick Time Events can die in a fire.
4. Fetch quests, particularly at the end of a game, can also die in a fire.
5. Gameplay bullets ≠cutscene bullets.
Specific Flaws (some are nitpicking):
1. In Ocarina of Time, Kaepora Gaebora's "Do you want to hear what I said again?" No and go away. To be more specific, he's so long-winded and rarely says anything of real value. The default option should be whatever allows the player to continue rather than repeat.
2. In Final Fantasy VII, you can't skip the summon animation. Final Fantasy IX only shows the full one at random which is better but still bogus.
3. Swimming in Resident Evil Revelaitons.
4. Sinking like a rock in the Great Bay stage in Super Smash Bros. Melee. Additionally, hit detection is off at times. It was a launch window title, this gets a pass.
5. Athena's characterization doesn't make sense at the end of God of War III. If the evils from Pandora's Box corrupted the gods when Kratos opened it at the end of the first God of War, Athena's personality is way off in the next two games. Characterization in the series is a problem. Kratos never evolves as a character. They tried a little bit with his relationship with Pandora toward the middle to end of God of War III, but it felt too late at that point. Also, the entirety of the hades stage of God of War.