As the affordability and the diversity of marine robotic platforms grow, the need for standardized software architectures, communication protocols and operating procedures becomes more critical. Going towards this direction, the Marine Autonomous and Robotic Systems (MARS) group of the National Oceanographic Centre Southampton started the development of a new on-board control and autonomy system, with the aim of delivering a modular and easily maintainable software that can be deployed on all the different platforms of the fleet. This paper presents the architectural description of the system, and the details on the implementation choices made to obtain a flexible and unique software ecosystem. As part of this redesign, two critical components have been completely re-designed: the mission executive layer, based on Behaviour Trees (BT), and the vehicle health management and diagnostic system. Details on these two key components are reported. Results from the first experimental campaign conducted in March 2019 in Portland harbour (Dorset, UK) with the newly developed ALR1500 vehicle provide some examples of the functionalities of the new system.