Systems Engineering is an ubiquitous discipline of Engineering overlapping industrial, chemical, mechanical, manufacturing, control, software, electrical, and civil engineering. It provides tools for dealing with the complexity and dynamics related to the optimisation of physical, natural, and virtual systems management. This paper presents a review of how multi-agent systems and complex networks theory are brought together to address Systems Engineering and management problems. The review also encompasses current and future research directions both for theoretical fundamentals and applications in Industry. This is made by considering trends such as mesoscale, multiscale, and multilayer networks; along with the state-of-art analysis on network dynamics and intelligent networks. Critical and smart infrastructure, manufacturing processes, and supply chain networks are instances of research topics for which this literature review is highly relevant.