The current FEP system rewards raising your stats evenly, which might make you think equates to a balanced diet, however what I'm noticing is that because I want to control which stat is raised to avoid being punished, I tend to eat only the one item (whatever is the highest FEP food for that stat) and eat tons of it, until I get the stat point.
I don't really have a solution to offer, I'm just pointing out, that eating a whole chest full of raising muffins doesn't seem like a particularly 'balanced' diet.
Maybe if there was some sort of bonus for having multiple colors in your FEP bar, or some sort of diminishing FEP return for eating heaps of the same thing (or both) that would encourage me to mix up my foods some more.