One thing that I really like with the Alkaline and Quoth mods that is also present in Quake II, is enemy skins showing “damaged” states whenever they are injured.
Anyway, going further down the rabbit hole, of how to push the bleak, dystopian science fiction feel of Quake I base maps, is to take a page from Silent Hill, and use the fog effect for outdoor environments like some mods already do, and portray the skyboxes as being overcast, dim gray skies as you see in Silent Hill 2.
Also, the stainmaps for some engines like FTEQW or Darkplaces should be used when damaging enemies. I do not know why the “blood” of Quake II enemies is so orange.
The enforcer’s weapon should be lootable and be the “hyperblaster” of Quake I, and as it would run on cells, cell ammunition should be more plentiful.
The normal grunt would be equipped with a pistol instead of his crappy shotgun to serve as an additional source of pistol rounds, and so he would need some sort of custom model and animation for firing his pistol. Then next up, you would have double-barreled shotgun wielding grunts filling the gap between pistol grunts and nailgun grunts.
There should be an enemy type that is actually equipped with the Thunderbolt in-game instead of the shambler being the only enemy that has a lightning attack…like a “Colonel” enforcer variant. Due to how damaging his weapon would be, he might be suited as a sort of miniboss, and therefore might have more health than a normal enforcer. I do not know what color his suit would be, but how about something like a black-and-yellow “hazard stripes” theme? When they spot you, they could yell something like: “TIME TO FRY!”
Enemies should also be damaged by falling in slime or lava in Quake I just like they are in Quake II.
Plus, just like Alkaline has cyborg fiends, how about shamblers with a cyborg skin?