As has been hinted at by other commenters, I think the big thing that's wrong with modern industrial agriculture (including some "organic" agriculture) is that

As has been hinted at by other commenters, I think the big thing that's wrong with modern industrial agriculture (including some "organic" agriculture) is that it typically does not add carbon to the soil (via composted plant matter, manure, etc) and it also unnecessarily disturbs the soil structure, allowing the organic carbon compounds in the soil to become excessively exposed to the atmosphere where they'll break down or be eroded. (No, I don't have specific sources for this, it's mostly a combination of what I've read from the Permaculture folks and personal observation in my own garden over the past 5 years.)