I wouldn’t mind seeing a background element to food that breaks each food item into different ‘food stats.’ These would be invisible to the user and can be safely ignored as long as you maintain a relatively balanced diet, but if you drop below a certain threshold (or go above a certain threshold) you get negative modifiers such as…
Protein: If you are low on protein you get a ‘Protein deficiency’ modifier which imposes a significant penalty on healing while sleeping, and you get tired more easily. There is no penalty or bonus for having extra protein.
Calories: If you are low on calories then you get a ‘Calorie deficiency’ modifier which makes you become tired more quickly, and you get hungry more quickly. If you have too many calories you get a ‘Too many calories’ modifier which imposes a movement penalty until your calorie level drops back into a healthy range. Generally speaking, high calorie foods should also be the foods that provide the largest mood bonus.
Vitamins: If you are low on vitamins then you get a ‘Vitamin deficiency’ modifier which lowers your resistance to disease and poisons, and can develop into mood swings (as the flaw) which remain until the vitamin issue is resolved, scurvy (which causes tiredness and pain and can only be cured specifically by consuming some amount of fruit), or migraines (reduced perception and intelligence, pain, and unable to read unless under the effect of pain killers), which come and go until the vitamin issue is resolved. Heightened levels of vitamins can give a mild bonus to disease resistance but also comes with a risk of developing mood swings until the vitamin level returns to the healthy area.
Disclaimer: this wouldn’t be something which would pop up a lot. It’s there to penalize people who stick to an all-meat diet or what have you, and would take a couple of days of poor eating to kick in the negative effects as vitamin levels or whatever gradually decline. The idea isn’t to force people to micromanage, it’s there to discourage people from settling into a routine of collecting squirrel meat from pits for all their food needs. The ‘healthy’ threshold would be quite wide and allow for brief periods of excess (found a bunch of oranges and apples) to sustain through relatively long periods of going without. Very occasionally it might pop up if you haven’t been eating enough of something, and it will give you a reason to go looking for a certain kind of food - that’s not a bad thing. And hey, at least it won’t be as urgent as an infected bite when you don’t have antibiotics.
It would be possible to add a ‘Severe deficiency’ of all of these with more alarming consequences, but one step at a time.
One issue with this model is that there are existing mutations which restrict or expand your diet. I think there are different ways to handle this. The easiest (and least realistic) way of handling it would be to drastically reduce the requirements for certain types of food stats for certain mutations. Like the carnivore mutation could have drastically reduced vitamin requirements because they can’t eat fruits and vegetables to get them. They would basically need to be able to satisfy their vitamin threshold using the small amounts of vitamins in meat.
Herbivores would be much the same, just regarding protein in plants. The rotten food one (forget the name) simply doesn’t get sick from/vomit from/take a massive mood hit from rotten food like others do. The stats of rotten food would simply be a somewhat reduced version of the fresh food - it’s just that most people have trouble keeping it down and not getting sick from the ‘extra’ crud in rotten food. This method would require some careful balancing.
A more time-consuming (and more realistic) way of handling it would be to give each food item a different set of stats depending on your diet. Carnivores would simply get more vitamins from meat than omnivores, and herbivores would get more protein from plants, but their thresholds would remain the same. This would at least be easier to balance, but I’m not sure it’d be worth all the work of giving every food item three sets of food stats.