as far as i know both filty clothes and magasines and nutrition can be disabled in options if you dislike them.i personally dont mind amd like added realism and they didnt infleunce my game at all but i have specific play style-melee character who use almost exlusively self made clothes though i dont mind using some fllthy clothes for temporary or desperate protection when my clothes get teared apart.
As for npc i basically turn every game i play into squad simulation with my npc team doing most of killing for me.with added pikcup options some of food managemtnt is eliminated but more can be done especially their annoying running from you as you finish quests and must chase them with cars to tell them you finished.
as per filthy clothes i find their color usefull in searhching for objects other than clothes.their penalties are small basically naglible and i dont know whats the fuss.simple make your own clothes or get clean ones in buildings.cleaning them is aslo not that difficult.on normal difficulty its quite easy to raid houses on edge of town and get some clean clothes to absolve morale penalties.
steel booms are probablly thing which inflenced my game most and make problems with recovery of damaged heavy vehicles.but as avaible heavy vehicles were basically middle end game for me i kind of like added difficulty in obtaining them.
I would like all of them to stay in game and if most people mind their existensce they can be mods for difficulty.