The development of intermodal transportation (IT) systems is of vital importance for the sustainability of logistics activities. The existing research point at individual directions of action for system improvement and increase of IT participation in overall transportation, thus reducing negative impacts of logistics on sustainability. However, there is a lack of research defining complex scenarios that unite existing ideas and concepts of IT system development and improvement. Accordingly, this article deals with the definition and selection of the most appropriate IT development scenario for the region of Southeastern Europe. Six different potential scenarios that differ in the network configuration, the required level of logistics infrastructure development, the role of different IT terminal categories, the involvement of different transportation modes, and goods flows’ transformation degree, are defined. The scenarios are analyzed according to four stakeholder groups and twelve defined criteria. A novel hybrid multi-criteria decision-making model, based on fuzzy Delphi, fuzzy Factor Relationship (FARE), and fuzzy Measurement of Alternatives and Ranking according to Compromise Solution (MARCOS) methods, is developed for solving the problem. The definition and analysis of the problem, the way of establishing the scenarios, as well as the development of a novel hybrid model are the main contributions of this article. A significant contribution is also the consideration of the Dry Port (DP) concept for the first time in the context of river ports. The results indicate that the scenario referring to the development of the IT core network with the Danube DP terminals is potentially the most appropriate scenario for the Southeastern Europe IT system.