I’m not a nutrition expert and am not qualified to give nutrition advice, but I can share my own self-experiments. 
This is just how I eat at the moment:
I don’t take supplements or fortified foods, except for 2000mg of vitamin D (doctor prescribed it), a probiotic, and fish oil capsules (2000-4000 mg of omega 3s per day, but this is due to trying to manage health problems). (2020 update: I switched to just vitamin D.)
I avoid refined food and mostly eat whole foods that I’ve cooked from scratch. I tend to cook things in advance like in the photos below and then mix the ingredients to create various dishes (restaurant style). That helps ensure that I don’t run out of quick access to healthy foods.
Those photos are from when I was eating only two giant salads per day (low starch vegan + fish diet). I’ve stopped that experiment and have tried to eat just one large meal per day (including grains and meat but no dairy) plus a snack, but I think that is ending now. I also do a water fast for 3-5 days per month.
I can’t recommend these extreme experiments – I’m doing them out of health necessity. Some of the experiments work better than others.
My protein intake is probably too low at the moment. I will increase the legume intake to cover that.
I’m hoping that using vegetables as a main staple ensures that I get enough nutrients. Eliminating empty calories (refined grains, sugar, etc.) means a higher amount of the nutrient-dense food.
I’m 70 pounds lighter than I used to be. My BMI went from “obese” to normal. I still don’t have my diet exactly right for my situation, but it’s working much better for me than when I didn’t have a system.