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.
Doom 1993 I do not like Episode 2 very much. Episode 1 has masterful level design, and Episode 3 has the abstract hell levels that are visually interesting, even if they aren’t that great to play. Episode 2 is just kind of boring. It does have the Tower of Babel tho, that’s a highlight.