This report represents deliverable D4.2 “System Release 2” of the R-WAKE project, which describes the final system resulting from WP4 (System Development) intended to support the research objectives and scope to be addressed as central task of WP5 (Simulation and Analysis). WP5 stands as the user of the system, with the central objective of providing an evidence-based proposal for either maintaining current separation-standards, or adopting new potential separation improvements, that is, the R-WAKE Concept(s) to be further investigated. The report includes an update of the research objectives and scope, in terms of research questions and targeted study scenarios, which incorporates the recommendations discussed during the mid-term review of the project. The R-WAKE project addresses the SESAR 2020 Exploratory Research work-programme topic ER-07- 2015 - Separation Management and Separation Standards, within the area of Advanced Air Traffic Services (ATS). The R-WAKE project overall objective is to investigate the risks and hazards of potential wake vortex encounters in the en-route airspace, in current and futuristic operational scenarios, in order to assess potential enhancements for the Separation Standards and Separation Management methods in Europe.