The bucket on an NPC's head while you rob them blind is my favorite example of a shining success of the line-of-sight system while simultaneously being a spectacular failure of basic AI.
The other nasty bug involving pixelization that we did manage to fix before shipping, but that I unfortunately didn't save any video of, involved the maid NPC, who was originally programmed by a really brilliant summer intern, but had a few quirks:
A Sim would need to go potty, and walk into the bathroom, pixelate their body, and sit down on the toilet, then proceed to have a nice leisurely bowel movement in their trousers. In the process, the toilet would suddenly become dirty and clogged, which attracted the maid into the bathroom (this was before "privacy" was implemented).
She would then stroll over to toilet, whip out a plunger from "hammerspace" [1], and thrust it into the toilet between the pooping Sim's legs, and proceed to move it up and down vigorously by its wooden handle. The "Unnecessary Censorship" [2] strongly implied that the maid was performing a manual act of digital sex work. That little bug required quite a lot of SimAntics [3] programming to fix!
Speaking of physics, the giant striking you with a hammer and launching your body into orbit.
And of course, can’t forget the classic Skyrim pathfinding jank. The number of enemies that would go aggro only to get stuck on a bush or a slight change in elevation while you stand there at a distance peppering their face with arrows until they die.
Your examples are from 10 or more years earlier that Skyrim's creation engine.
That is to say, the older engines could have been limited by hardware requirements, or maybe decoupling physics from fps is an innovation that appeared between 2004 and 2011. Or maybe they are also jank.
Notably, the source 2 engine (2015) decoupled physics from fps (as I understand).
You answer your own question! Not remotely to the same extent. Quake, for instance, gave a small advantage for jump height [with high FPS]. Skyrim would outright break.
Also, you've listed three generations of the same family; goldsrc, the child of Quake, predates Skyrim/Creation by at least a decade. Of those, Source would be the timely match. Not even close to the same amount of jank. Just... no. You aren't tricking me into writing lists.
I don't really intend to be critical of Skyrim, like many: I love the jank. It's expected. It's a Bethesda game.