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.
Half-life’s Xen levels are particularly infamous for this sort of thing. There’s a reason the Black Mesa remake overhauled it.