I love the original Hotline Miami but I’m not a big fan of the boss fights like the ones in Neighbors (Biker) and Deadline (Van Driver). I find it kind of slows down the game and limits the strategies you can take.
Another example would be Fallout 3. I find the tutorial section in Vault 101 can feel a bit long after a fifth run but maybe that’s because I was spoiled by Fallout New Vegas’ ability to run off in your own direction immediately after leaving Doc Mitchell’s house.
The Great Tree in Paper Mario: The Thousand Year Door is the worst dungeon by far. The puzzles involve escorting a bunch of NPCs that can’t jump, run away from enemies, and inconsistently break away from following Mario.