(DISCLAIMER: I have yet to read the remaining two posts, but I have some thoughts based on part one.)
Half-Life + STALKER + Fallout + Metro threats? Amazing!
I completely agree with you that UII should take on a more horror oriented direction.
Now, some of my suggestions are:
The greenish colour palette for the Turned should be dropped imho. A pinkish, flesh-like design feels far more natural and organic, and far more terrifying. Also, alternatively black as the main colour could work.
More deformed/Non humanoid enemies:
Arachnoid, ameboid, insectoid horrors that crawl around could really spice things up from both gameplay and horror perspectives. For example Spider like creatures that are affected by the sickness, although not influenced by the Hivemind, that have underground dens.
A great emphasis on sounds and Turned vocalizations can greatly increase the horror factor, and when we are at that, neutral turned could have a wide array of vocalizations, such as weeping, attempting to speak, but failing and similar activities that display the remains of their former selves.
Sorry for terrible formating, mobile is not very user friendly 