What are the "obvious limitations"? There are many problems with today's industrialized agriculture, but I wouldn't call the limitations obvious. The article says it doesn't work well in Africa for instance, and I believe it, but isn't it just because we don't have the proper GMOs/fertilizers/pesticides for this kind of soil due to a lack of interest? Is there some "obvious limitation" that makes it impossible.
I am not criticizing agroforestry. It is not like I want pesticides, artificial fertilizers and lifeless fields. But they cite 1920 as the starting year for the beginning of modern agriculture. During that time, the world population went from 2 to 7 billion. If we want do bring back ancient techniques, we have to do it in that context.
I often see the forest treated as an example of an efficient for of agriculture, and sure, forests are really dense with life. However, they are like closed systems, everything that is produced by the forest is used by the forest. Now, what we want is a patch of land from which we can pull as much as possible in order to feed our cities. There may be trees, but it won't be like a natural forest.
To make things clear again, I don't view agroforestry as a bad thing. If it allows good yields on previously unexploited land and does it so while preserving biodiversity, what's not to love. I am just skeptical when considered as a substitute for modern industrial agriculture.