I think the problem with most GMO debates is the assumptions coming from both sides. The GMO proponents place the only viable means of food production as industrial agriculture. If that is the way forward, unmodified and naturally selected plants have a disadvantage because they didn't evolve to be farmed in massive monocultures on poor lifeless soils.
If small scale, intensive, regenerative farming is the way forward, GMOs are at a disadvantage. They present no benefit to the farmer, but come with extreme costs and no ability to save seeds and improve varieties to the specific climate, soil, and ecosystem.
So the argument, to me, shouldn't be held on which method of breeding plants is superior, but which method of growing is more sustainable and liberating for the communities. Pesticides and herbicides are a portion of the problem. Tillage, soil erosion, demineralization, pollution and depletion of the ground water, rivers, and lakes, are all issues that we should be concerned with.