There are many methods for plant propagation. While seeds have remained the main method of propagating annuals, other methods have become the preferred means of propagation in the culturing of trees, shrubs, bulbs, etc. Layering, cuttings, divisions, grafting, and other clonal means of reproduction are fast and produce consistent results; these are the demands of industrialized food production but not consistent with the ultimate furthering of agriculture. Cloning in various forms creates a genetic homogeneity and limits genetic potential. Consistency can be a weakness as well as strength; uniform susceptibility to disease and pests for instance. While grafting trees together may allow for more vigorous plants in the present; those benefits can never be passed to their offspring. In addition, if a grafted tree produces fruit its seeds do not usually produce viable offspring.
The reasons one would choose seeds for propagation are the same evolution has chosen sexual reproduction versus clonal or symbiotic. Every seed represents an entirely new genetic individual. Because plants sometimes have multiple copies of large chromosome numbers sexual reproduction produces more variety than seen in organisms such as humans. While reaping increased harvests of improved quality is not ensured from planting seedlings it is at least possible. Working with limited genetic resources (cloned, grafted, etc.) boxes one in regarding potential. It should also be noted that an offspring is likely to be equal or improved regarding the two parent individuals; this is the reason sexual reproduction exists. Artificial selection via humans can rapidly hone new desirable traits found through sexual reproduction.
Resistance to stochastic events such as heat, drought, disease, pests, etc. also varies between seedlings. As climate change increases the frequency of these events it important that the system be able to adapt and evolve . The genetic capacity to deal with tremendous changes over time is a signature of true resilience. If permaculture systems, particularly orchards, are to be self-replicating systems that evolve over time, then seeds are the only means of creating that genetic resource base.