Aside from the continued use of chemicals, my biggest concern is the genetic pollution of natural populations with engineered genes. The escape of herbicide resistant genes from crops to their wild relatives will create new weeds and disrupt ecosystems. Genes have mobility. They move from organism to organism of the same species during reproduction. Encapsulated in pollen grains, they drift in the spring breeze and coat the bodies of insects.
Pollination is promiscuous business.
Wind-dispersed pollen lands indiscriminately on all kinds of plants. Pollinating insects visit many species of flowers, not just one. Because the reproductive barriers in plants are more lenient than in animals, it is possible to transfer genes between different species. Successful cross-pollination is further made possible by the close proximity of compatible species. Remember that agriculture emerged as a result of domesticating wild, native plants.