Considering the trend seen in recent years regarding drones and their applications in the near future, it becomes clear that more and more systems will be created to support the use of UAVs. This paper presents the integrated Model-Based design approach employed for the development of DIVE (Drone Integration and Validation Ecosystem): a System of Systems (SoS) designed as a functionalities-based architecture. This design technique has been chosen to reduce the time to market new systems since it allows to lower the number of iterations during development, hence facilitating the development and integration of new UAV systems. Currently, DIVE comprises four main areas: Mission Planning, Validation, Operations, and Safety. SkyMission, ARMONIS (Aircraft and Remote MONitored Integrated System), and ELITE (Emergency Landing Identification and Termination System) are the systems that cover these modules. DIVE and the systems it comprises are tested in a digitalized world, exploiting the concept of digital twins, and Wire, the framework that connects them. SkyMission is a simulation environment, created to study and test mission scenarios with UAVs. ARMONIS is a versatile platform meant to permit direct teaming between aircraft personnel, unmanned vehicles, and ground operators. ELITE is a system for UAVs that, unlike a common FTS, employs state-of-the-art Machine Learning and Computer Vision technologies to determine the best termination area on the terrain. The underlying backbone that connects all those modules is Wire, a distributed communication framework that can exchange data between them in a decoupled and efficient way. The first tests for these applications with the digital twin have shown promising results. Leveraging different systems, DIVE will be a reliable and scalable system of systems developed using a Model-Based approach, for the integration of UAV-based applications, establishing a novel functionalities-based ecosystem.