The paper presents the initial outcomes of a project, currently ongoing under the supervision of the European Space Agency, having the main objective to specify and design a Fault Detection Isolation and Recovery (FDIR) system by making use of relevant RAMS (Reliability, Availability, Maintainability, Safety) analyses for missions in non-deterministic environment with limited resources. The initial project tasks have been to select a study case represented by a CubeSat complex mission, analyse in detail both its mission and system requirements and, based on them, define a set of relevant RAMS analyses to be carried out in the second phase of the project, as inputs for the development of a FDIR concept aimed at a careful balance of the limited spacecraft resources in case of critical failures. Two possible study cases have been identified: LUMIO, a 12U CubeSat mission for the observation of micro-meteoroid impacts on the Lunar farside, and M-ARGO, a 12U deep-space CubeSat which will rendezvous with a near-Earth asteroid and characterize its physical properties for the presence of in-situ resources. Although both missions are characterized by a high level of autonomy and complexity in a harsh environment, LUMIO has been eventually selected as study case for the project. In the paper, the challenges and features of this mission are shortly presented. The specificities of the RAMS analysis and FDIR concept for this specific class of small satellite missions (including the selected study case) are highlighted in the paper, looking in particular at aspects such as the improvement of reliability while maintaining the CubeSat philosophy, the tuning of mission and system requirements in view of facilitating the design and implementation of the FDIR concept, and the current gaps within the RAMS/FDIR body of knowledge. The conclusions drawn during this first project phase provide a real view of how systems engineering must work in tandem with RAMS analyses and FDIR to achieve a more robust and functional mission architecture, thus improving the mission reliability.