In this paper we introduce a technique to reduce the effects of uncertainty and incorporate flexibility in the design of complex engineering systems involving multiple decision-makers. We focus on the uncertainty that is created when a disciplinary designer or design team must try to predict or model the behavior of other disciplinary subsystems. The design of a complex system is performed by many different designers and design teams, each of which may only have control over a portion of the total set of system design variables. Modeling the interaction among these decision-makers and reducing the effect caused by lack of global control by any one designer is the focus of this paper. We use concepts from robust design to reduce the effects of decisions made during the design of one subsystem on the performance of the rest of the system. Thus, in a situation where the cost of uncertainty is high, these tools can be used to increase the robustness, or independence, of the subsystems, enabling designers to make more effective decisions. This approach includes uncertainty caused by control factor variation (Type II robust design) and uncertainty caused by unknown nonlocal design information (Type I robust design). To demonstrate the usefulness of this approach, we consider a case study involving the design of a passenger aircraft.