With all this talk about gm crops underperforming, I think people forget that the common GM crops were not modified to increase yields. This is also something the right forgets when it trumpets GM crops as some great solution for this food crisis.
Fundamentally, GM crops are easier to manage. Last week in one of my classes, some of the students from farms were talking about how they used to have the arduous job of "walking the beans": meandering out in the soybean fields in the hot summer sun, looking for weeds to spray. Now they just douse the entire field every once in awhile. They brag about how nice their fields look.
To contrast, managing an intercropped organic field requires intense labor and finely honed knowledge.