Lack of collaboration between individual systems and system of systems (SoS) program management is identified as one of the leading problems in SoS acquisition. This is especially a major concern in acknowledged SoS where a designated SoS program management has no authority over the constituent systems. Therefore, it is important to consider mechanisms to persuade individual systems to participate in the SoS development. In SoS where individual systems have their own self-interests, negotiation becomes an important mechanism to increase participation in SoS development. Another mechanism, incentives, is used in a wide range of applications to improve performance and collaboration. In this paper, an incentive based negotiation model is outlined as a mechanism to increase participation of individual systems into the SoS development. The negotiation model is integrated into an SoS Engineering and Architecting multilevel model referred to as Flexible & Intelligent Learning Architectures for SoS (FILA-SoS). Various aspects of SoS acquisition are modeled in the FILA-SoS including SoS metaarchitecture generation, evaluation as well as negotiation between SoS and individual systems. Individual systems exhibit behaviors, ranging from selfish to cooperative. The negotiation model is demonstrated on an SoS engineering application: Intelligence, Surveillance, and Reconnaissance (ISR) SoS acquisition case where a desired meta-architecture is selected for negotiation, and incentives are determined for systems based on deviation from the desired meta-architecture quality. The analyses of the results from this application domain provide insights into how incentives can be used by decision makers to increase participation in SoS engineering and development. C⃝ 2015 Wiley Periodicals, Inc. Syst Eng 18: 310-321, 2015