I ran through Doom 3 yesterday since I'd never fully beaten it.
Most of the enemies I found fine, or at least reasonable. The archviles were obnoxious, but fill a niche, and only really come into play once the soul cube is acquired. They spawn the charges, are used sparingly and it works well.
The cherubs were annoying, but are an upgrade on the trites to counter the availability of ammo, and blend in with the shadows. I imagine if I had played the original release, they'd be the most annoying, but BFG edition's suit flashlight meant I could pick them out.
No, the most annoying have to be the ZSec assault rifles/shotguns and the commando chaingunners.
When you take damage, the screen flips out to a ridiculous degree, meaning any aim you had is thoroughly fucked. When fighting strong demons and dodging fireballs, it makes sense. Spasming from a single rifle shot to power armor just kind of ruins it, and makes the demons seem weaker by comparison. It doesn't help that ZSec and chaingunners don't react to damage but maybe once as their health dimeneses. So keeping accurate fire on them is almost impossible in a straight up fire fight, but they can easily focus in on you.
The shotgunners also fire faster than the shotgun cycles.
Pistol ZSec balance it out by having a slow rate of fire, but more mobile. They're more accurate than other ranged enemies and harder to hit, but do less damage overall and add a new challenge. The other ZSec just seem to be there to force players to crouch behind walls.
Chaingunners take all of those issues and increase it by having a more powerful, longer range, faster firing weapon with increased health. Seeing as how most of the mid to late game encounters focus on running around claustrophobic arenas where standing still gets you killed, incorporating enemies whose only counter is cover based long distance fighting is a bit counterproductive, making the better equipped ZSec and chaingunners the worst enemies to fight in Doom 3. Hadn't been that frustrated with enemy design in a while, but it could be due to playing through the whole thing in a day.