I've read that the amount of protein in wheat has been declining for a century.
I remember 40 years ago rye bread was really dense and rich. Now it takes like rye flavored white bread. Also bread now tastes suspiciously sweet to me.
Other common staples like corn and rice had hundreds of varieties in the past, many of which are extinct or only exist in a seed vault. The same is true for fruits. If you travel to particular developing countries or even just to Hawaii (where native varieties are protected), you'll see how different their fruits and vegetables are - both in variety but also smell and taste. I'm sure that has nutritional implications that simplistic reductionist nutrition approaches can't capture.
I remember 40 years ago rye bread was really dense and rich. Now it takes like rye flavored white bread. Also bread now tastes suspiciously sweet to me.