In an increasing competitive market where offer exceeds demand, developing customer value is nowadays a key driver of industrial activities. Reducing costs, increasing quality, deliver on time and the introduction of the right product quickly are unavoidable elements to succeed. A higher product variety for mass production and short lead-time are main features of mass customization. Flexibility arises as a productive and competitive factor to face it, of particular interest in assembly systems, which allow the postponement of final variety, integrating all former tasks of the supply chain. In this scenario, flexibility helps to face uncertainty in decision-making, while the increase of system complexity requires extra control and management efforts. Both flexibility and complexity are briefly reviewed. Next, it is introduced a joint analysis of flexibility and complexity useful for decision-making. Both are linked to the uncertainty of the possible states of the system and a quantitative approach of general application is presented. Finally, based on a model simulation, a first case application illustrates product variety increase in an assembly system and some decision-making trade-offs.