In embarking towards Cyber-Physical Systems (CPS) with unprecedented capabilities it becomes essential to improve our understanding of CPS complexity and how we can deal with it. We investigate facets of CPS complexity and the limitations of Collaborating Information Processing Systems (CIPS) in dealing with those facets. By CIPS we refer to teams of humans and computer-aided engineering systems that are used to develop CPS. Furthermore, we specifically analyze characteristic differences among software and physical parts within CPS. The analysis indicates that it will no longer be possible to rely only on architectures and skilled people, or process and model/tool centered approaches. The tight integration of heterogeneous physical, cyber, CPS components, aspects and systems, results in a situation with interfaces and interrelations everywhere, each requiring explicit consideration. The role of modelbased and computer aided engineering will become even more essential, and design methodologies will need to deeply consider interwoven systems and software aspects, including the hidden costs of software.