I think you may have hit on part of the answer in the questions that you are asking. I was hoping to see some other commentor mention just exactly what these stone tools were used for and therefore what effect they had on our bodies. While you can use Stone to make all kinds of tools including mortars and pestles, which would help with processing grains and vegetables, the primary kind of stone tools that you’re referring to here are projectile points. They were used to kill animals. This suggests that starting close to 3 million years ago our diet changed dramatically. From being seasonal frutarians and opportunistic gatherers throughout the year, we were able to bring down much larger animals and have a nearly continuous supply of meat. So when you ask, what kind of nutrient might you be missing out, I don’t think it’s that you’re missing anything (as long as you eat meat) because we have been adapting to a highly meat-based diet for a very long period of time. Only since the onset of agriculture 10 to 15,000 years ago, did our diets start to shift towards grains. The consequence of that is pretty clear, obesity, see the Venus figurines, and diabetes and all of the diseases that excess calories can lead to.
I think you may have hit on part of the answer in the questions that you are asking. I was hoping to see some other commentor mention just exactly what these stone tools were used for and therefore what effect they had on our bodies. While you can use Stone to make all kinds of tools including mortars and pestles, which would help with processing grains and vegetables, the primary kind of stone tools that you’re referring to here are projectile points. They were used to kill animals. This suggests that starting close to 3 million years ago our diet changed dramatically. From being seasonal frutarians and opportunistic gatherers throughout the year, we were able to bring down much larger animals and have a nearly continuous supply of meat. So when you ask, what kind of nutrient might you be missing out, I don’t think it’s that you’re missing anything (as long as you eat meat) because we have been adapting to a highly meat-based diet for a very long period of time. Only since the onset of agriculture 10 to 15,000 years ago, did our diets start to shift towards grains. The consequence of that is pretty clear, obesity, see the Venus figurines, and diabetes and all of the diseases that excess calories can lead to.