Based on a socio-historical analysis of changes in the French peach and apricot industry since the 1960s, and on the place of genetics and cultivar breeding in this trajectory, we describe the shift from an innovation model based on criteria linked to the production stage to an innovation model based on marketing criteria (fruits’ ability to be transported and stored and fruits’ visual aspect) and explore its consequences. Although the modern cultivars are most often disappointing for consumers, rather unsustainable for the environment and not always such a good choice for producers on the long term, why have societal pressures for sustainability continuously failed in really impacting the breeding system so far? A study of recent changes in public research and in cultivars’ evaluation and registration with a focus on the controversies in several “mainstream” or “transition” arenas leads us to suggest a balanced answer to this question.