In recent times, there has been a rapid surge in the advancement of technologies associated with Unmanned Aerial Vehicles (UAVs), particularly in the domains of sensors, networking, and processing. Consequently, substantial investments from both governments and industries have been directed towards the exploration of UAVs, aiming to enhance their performance for secure and dependable deployments. The evolution of design methodologies and the exploration of UAV systems have transitioned from single UAV applications to encompass multi-UAVs and cooperative UAV systems. These systems necessitate a heightened level of coordination and collaboration to execute tasks, demanding innovative networking models, approaches, and mechanisms tailored for highly mobile nodes, encompassing numerous intricate parameters and constraints. The present paper provides comprehensive insights and conducts a meticulous examination of UAV communication protocols, networking systems, architectures, and applications. Furthermore, it delves into UAV solutions while underscoring critical technical challenges and unresolved research issues that warrant further investigation and dedicated research and development endeavors. In this paper, we study some problems and solutions for The Command and Control (C2) aspect of UAV communication systems. We also give some directions for research in near future.