The paradigm shift to focus on an enhancement of existing aircraft systems raises the question which of the many possible incremental improvements results in an advantageous solution still considering all existing requirements. Hence, new methodologies for aircraft system design are a prerequisite to cope with such huge and complex design spaces. In the case of flight control system optimization, major design variables are the control surface configuration and actuation as well as their functional allocation. Possible architecture topologies have to be verified inter alia with respect to system safety requirements. In this context, flight dynamic characteristics and handling qualities of the fully operational as well as of several degraded system states of each topology have to be evaluated and checked against common specifications.A model-based verification of the requirements is favorable, resulting in a rapid reduction of the design space. Safety objectives for valid configurations are derived and serve as an input for a subsequent safety assessment. This two-step methodology, a simulation-driven verification of handling quality requirements and a corresponding safety assessment, is presented in this paper. The methodology is intended to support the design engineer in the early concept phase of the system architecture development process.The handling quality analysis is based on a generic flight simulation environment. Using parametric library components, various aircraft and system configurations can be modelled and automatically evaluated via an associated tool suite. Furthermore, an in-house developed analysis tool for system safety is used to carry out the safety assessment based on reliability block diagrams of the flight control architectures.To validate the proposed methodology, an existing, conventional hydraulic-powered flight control system of a single-aisle short-range aircraft is evaluated with respect to its design and safety margins.