Engineering an enterprise system as a whole from business to manufacturing to fulfill capabilities in order to achieve global performances remains in fine a complex ad hoc process. This complexity is addressed by many modeling artifacts ranging from top down enterprise modeling frameworks to bottom up COTS systems engineering approaches. Increasing manufacturing globalization and enterprises collaboration are impacting this large-scale systems integration, so that the SoS paradigm is challenging both academic and industrial communities to border the whole enterprise system for any new mission on the enterprises operational components. This paper addresses some system thinking issues about SoS as a candidate rationale artifact for enterprise information-intensive system modeling.