In recent decades, aquaculture nutrition research has made major strides in identifying alternatives to the use of traditional marine-origin resources. Feed manufacturers worldwide have used this information to replace increasing amounts of fish meal and fish oil in aquafeeds. However, reliance on marine resources remains an ongoing constraint, and the progress yielded by continued unidimensional research into alternative raw materials is becoming increasingly marginal. Feed formulation is not an exercise in identifying “substitutes” or “alternatives” but rather is a process of identifying different combinations of “complementary” raw materials—including fish meal, fish oil, and others—that collectively meet established nutrient requirements and other criteria for the aquafeed in question. Nutrient-based formulation is the day-to-day reality of formulating industrially compounded aquafeeds, but this approach is less formally and explicitly addressed in aquaculture research and training programs. Here, we (re)introduce these topics and explore the reasons that marine-origin ingredients have long been considered the “gold standards” of aquafeed formulation. We highlight a number of ways in which this approach is flawed and constrains innovation before delving into the need to assess raw materials based on their influence on aquafeed manufacturing techniques. We conclude with a brief commentary regarding the future funding and research landscape. Incremental progress may continue through the accumulation of small insights, but a more holistic research strategy—aligned with industry needs and focused on nutrient composition and ingredient complementarity—is what will spur future advancement in aquaculture nutrition.