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.
Ghost of Tsushima is one of my comfort games, but I hate replaying the end of act 2 because of the emotional toll.
In Devil May Cry 3, the Nevan boss fight and backtracking through the rearranged tower after it’s activated are just tedious.
Another user said the Fade section of Dragon Age: Origins, but I’ll go with the Deep Roads. Everything you learn in that section is fascinating, but man, I just want to see the sky again and you’re down there for a while.