As mentioned, dirtiness accumulation and waste disposal have pretty much been solidly shot down due to not being fun, it mostly boils down to “do you have certain resources and the time to use them?”. If you meet those requirements, it’s just tedium, if you don’t you get extra penalties you can’t do much about.
One way I could see that sort of thing being reasonable is if you had some kind of meta-action you can trigger once you establish a base camp, where you enter your home and trigger “make self at home” or similar, which means you change into fresh clothes, clean yourself, maintain tools (including weapons), reload guns and gear, cook and eat food, perform some leisure activities (reading, training, long-term crafting), all of which have practical and/or morale benefits. If it were shortened to such an automated action that consumes time and resources with minimal player direction (e.g. you get prompted when new facilities are available to “add action to your routine”) I could see it being beneficial, but that’s a lot of automation to do.
A plus of this approach is that it might segue into you assigning some of these tasks (tool maintenance, food prep) to NPC companions to do, freeing you up to do more important things.
I’m pretty in favour of deepening the medical system, even to the extent of having multiple varieties of antibiotics that are more or less effective on different infections. The tricky part there is the player needs access to some kind of resource that lets them determine which one to use without having to know all the intricacies of antibiotic interactions. Ideally access to that special knowledge wouldn’t even help, we don’t want to reward/force people for googling symptoms and finding out what antibiotic to use.
