The unnamed protagonist of Doom 3 is probably actually called "Marine Transfer", considering that is what appears on the passenger list at the start of the game (alongside Elliott Swann and John Campbell).
Classic Doom, the Arachnotron and Spider Mastermind have, compared to other monsters of similar strength, a disproportionately high chance of flinching when they're hit and being interrupted from shooting back. They're giant brains on mechanical legs. Of course they're going to be less resistant to pain.
Which has a bit of fridge logic in itself, since a brain is the ONLY part of a body that cannot feel pain at all (it processes pain but actual harm done to the brain itself can't be felt)
Possibly it's not actually pain, but unintended spasms caused by the punishment being rained upon them, then?
Also related is the fact there aren't any dogs in the secret levels. One wouldn't expect animals to be subject to the same punishment as the people that trained them.
The final boss of Doom II is John Romero's head on a stick obscured by a giant image of a Satanic monster called the "Icon of Sin". Appropriately, it is the source of all the monsters you've been fighting up to now, which of course is John Romero's duty as a game designer.
People complain about the huge, clunky PDAs used in Doom 3 as an example of zeerust when they should be using something closer to a smartphone, but it makes all kinds of sense when you consider the setting and context: It's an interplanetary mining operation involving joint private and military efforts, so they would issue their employees a heavy-duty, hard-to-misplace device with a highly visible screen and long battery life at the lowest possible cost.
The fight against the Cyberdemon at the end of Doom 3 is a call back to the final boss at the end of Doom 2. A small area filled with continuously spawning enemies and a boss that can only be hurt by one kind of attack.