Mass Effect 3 - the ending(s), duh
Twilight Princess - the tear hunting
Mass Effect 2 - the plot is generally nonexistent due to a focus on characters and worldbuilding
Metroid Prime 3 - spoken dialogue and increased focus on story is unnecessary
Breath of the Wild - missed opportunity to focus on the lore and world, lack of story and character development, not enough NPCs or a living world (this was an intentional design decision, obviously, as it's a post-apocalyptic world of sorts)
Super Smash Bros. for Wii U - frustrating roster cuts and other missing features from Melee and Brawl
The Wind Waker - the Triforce quest
Overwatch - poor balancing philosophy, lack of progression rewards or other features to encourage long-term play, no teambuilding/role queue feature until last week
Mass Effect - too many RPG elements like useless amounts of weapons and armor, clunky menu interfaces and combat that have aged very poorly
Metroid Prime 2 - dark world sapping your health and being extremely dangerous in general is an interesting concept but largely a pointless frustration, certain environments are bland and lack the color and character of Tallon IV
Life Is Strange - the garbage endings
Deus Ex: Human Revolution - the stupid boss fights
Super Mario Odyssey - repetitive moon quests across each world
BioShock Infinite - shitty "both sides" moral relativism that largely undermines any political point of the game, convoluted story that falls apart at the end
The Last of Us - repetitive combat environments that stick out from the rest of the world and ruin immersion
Monster Hunter World - post-game sucks and has nothing to do but fight tempered elder dragons and play the RNG game for decorations or relic weapons