I'm Just Gonna Post Doom Articles Until I Fall Asleep I Guess
An expansion on Warren's point about representation:
http://www.pastemagazine.com/articles/2013/12/20-years-of-doom.html
I'm surprised I can't find anyone write about Doom's specific design decisions any more in-depth than LeBreton, though. I want someone who understands this game way more than me to pick apart every monster.
Example: the Arch-Vile's two attacks are perfectly chosen for the tension they create with their overlap - the resurrect means you really really need to focus on it badly, but the blast attack means you really really need to stay out of sight. It makes fighting one an
event because you flip back and forth between two opposite states of ohshitohshitohshit. This kind of thing is surely common knowledge to Doom players, but it's written in hundreds of megawads and personal experiences, not in text.
This one comes close:
http://blog.danbo.vg/post/50094276897/the-most-misunderstood-game-of-all-time
(and I'd adore it for no other reason than it opens by calling John Carmack "id's last shred of credibility.") He nicely puts something that's just as true about Quake, which I've always had difficulty articulating: that the player in an FPS like this is fighting the level designer, and even if the enemies are dumb, their arrangement within local architecture and the overall arc of a level is where the intelligence is manifested.
Also, apparently the best Doom level ever is in fact E4M2. Need to scrounge up a copy of TFC again.