The world is facing an increasing level of systems integration leading towards Systems of Systems (SoS) that adapt to changing environmental conditions. The number of connections between components, the diversity of the components and the way the components are organized can lead to different emergent system behavior. Therefore, the need to focus on overall system behavior is becoming an unavoidable issue. The problem is to develop methodologies appropriate for better understanding behavior of system of systems before the design and implementation phase. This paper focuses on computational intelligence techniques used for analysis of complex adaptive systems with the aim of identifying areas that need methodology customization for SoS analysis.