Strijkbout: I like Doom but this article is laughable really.
Doom's main merit comes from it being the first to popularize the genre but that's mostly it.
Doom's superior leveldesign?
Thanks to its advanced game engine Doom looked very flashy when it was new but when you disect its levels it's just two thirds of futuristic spacebase levels with the same textures used over and over again and 1/3 of hell levels with textures used over and over again compare that to the levels from Dark Forces for example.
The rest is a matter of taste mostly, everyone has a different oppinion on how a good FPS should be.
Thing is, IMO the Doom levels would be a lot of fun even without any textures. Dark Forces wasn't bad - but it lived through oozing this Star Wars atmosphere and the badass Kyle Katarn. In terms of "actually playing it" it was never as much fun as Doom - aiming up and down was a PITA (no mouse support for that!) and you needed it for those darn ceiling mounted turrets in the later levels.
The same holds true for Quake (and to a lesser extend to Quake 2). Gameplay wise the levels were perfect - but with no sign of visual realism. The monsters were perfectly designed - each with their unique abilities and patterns.
Look at the games that were "speedrunned" the most - those are the ones that were truly outstanding in game/level design. And not from "being the first to popularize the genre".
Nirth: I very much agree with level design but not high skill ceiling. The first one is self-explanatory after seeing that lovely picture in the article but the latter is based upon my view of delusional superiority that automatically comes after winning, this is further enhanced when you view a game solely for winning and avoiding to lose and nothing in between (see also the expression "easy to learn, hard to master"). I see a challenge as a means to an end, thea idea to survive a problem like avoiding to become bored (this is important in entertainment) and if it's used well it's a nice, but not vital icing on top of a good cake (cake being the actual gameplay).
Doom/2 is/was one of the most popular game in the speedrunning scene. In fact I think the scene came from Doom with it's recording ability included. Watch some of the Grandmaster/Nightmare speedruns and then rethink what you wrote about "high skill ceiling".
ChrisSD: One thing the article mentions is the fact you only have to aim horizontally not vertically and you often have a wider hit box to target anyway. Considering how some people disagree with console game's aim helping mechanisms I'm surprised more people haven't disagreed on that point.
That point is something that really hinders me replaying Doom. Not being able to look up and down really annoys me. And when it's enabled (most source ports can do this) it somehow looks totally wrong.
Autoaiming is something that I always turn off if possible (ini-hacks, etc). In fast paced run&gun games I'm a rocket launcher junkie and I want to decide where I shoot (leading, splash damage tactics).
As for Doom - I guess in the old days many people still played with only the keyboard which is even more crude than gamepad, so that assistance was required for the same reasons it is today on consoles.