One of the major challenges in industrial production is to efficiently design or redesign a competitive manufacturing system (MS), as the associated decision-making process is very complex. The scenario of Industry 4.0, with rapid changes in key factors such as technology and costumer demand, has made such process even harder, and the need to structure it has become stronger. This paper analyzes how decision-making has been structured until now to design MS and highlights the main relations among decisions. Then it proposes some considerations about how Industry 4.0 is changing decision-making structures.