In my vision, the nutrition categories would be: carbohydrates, proteins, fat, fiber, and micronutrients. Most foods would give more than one nutrient category. Meats would give both protein and fat, for example, but no fiber or carbohydrates, and very little micronutrients.
"Dairy" being a nutrient category currently peeves me, in this system milk and cheese would still be useful as it would have everything except fiber and be one of the best sources of fat.
This system would also make it so that it would sometimes actually make sense to eat animal fat instead of hoarding it for crafting.
The most important part of this concept is the micronutrients category, currently there is not any incentive in the game to have a varied diet. Different foods would give different micronutrients, but what exactly they were would be hidden from the player. One kind of food could only raise the micronutrient bar so far, you would need to eat a wide variety of foods to fill it up all the way (so you can't just eat turnips forever).