Comparing classical plant breeding with GMO (or with the techniques used in the green revolution) isn't really that useful. There are too many technical differences between a process that uses selection which operates over hundreds to thousands of years, and a process which instantly changes the phenotype of a plant. And those differences matter a lot!

The only truly risky GMO I've seen was a case where the allergen from brazil nuts was accidentally introduced to experimental soybeans, which seemed to cause the soybeans to trigger brazil nut allergies in people. That was discontinued pretty quickly.