The question of when humans really started eating grains is a good one.  This Spartan Diet Blog post summarizes some newer evidence that grain consumption might have been more extensive earlier than people thought.  It does seem however that grains are a newer addition to the diet than say fruit and meat which primates still eat today, so I can see how proper preparation of the food might play a more significant role.  Also the genetics of a particular population and their gut flora/fauna might have evolved over time to make it more nutritious for them.  However today with all the global mixing of genes and food, the ability to digest something like dairy properly can no longer be expected to be confined to the places where dairy is readily available.  The use of fire for cooking also is thought to have played a significant role in what we ate and how much nutrition it provided.  A recent Spartan Diet post titled "The 6 qualities that transform bread from junk food to superfood" summarizes well with what I have been trying to do with the bakery.  Here are my comments on their list:

• Natural leavening and fermentation: I don't do this for all my breads, but some recipes have used some Vinegar which helps with some of the benefits of a Sourdough.  My 18+ hour soak of everything also helps achieve part of this goal.  I'll continue to experiment with new recipes in this area.
• Ancient grains: This is a long process to get there, but I have a great start with heirloom wheat, Khorasan (Kamut), Spelt, Rye, Oats, and others in the rotation.  It will take more work to get other old varieties grown, but I'm working on that and able to clean, store, and mill the novel varieties I do get my hands on.
• Organic grains: I'm always using at least chemical-free grains if not Certified Organic.
• Whole grains and Freshly milled flours: This has been my commitment from the start - flour that is milled only when needed and never sits at room temperature for days or weeks.  Sometimes my flour is sifted a little to remove some overly large pieces of bran, but all my breads have all the germ and still the majority of the bran.
• Zero non-food ingredients: It of course just makes sense to not add any preservatives or highly processed dough strengtheners and the like since I am going to all this trouble with the other ingredients.

The Weston Price Foundation has been around for a long-time and thoroughly explores the foods and cooking methods of traditional cultures.  To give you just one link, this very long post describes the many things we now do wrong with industrial bread production and the many better ways to make bread.  I haven't researched everything they say to see what agrees and conflicts with others so I still have plenty to learn in this area.  

Besides being nutritious and healthy for a given individual, I believe our food also needs to be produced in a local and sustainable manner.  I don't think it will do the majority of people any long-term good, to base their diet around an over-harvested wild food or food that is primarily non-local.  That is a perspective that I think a lot of "diets" totally ignore.