The rapid changes in today's socio-economic and technological environment in which the enterprises operate necessitate the identification of new requirements that address both theoretical and practical aspects of the Enterprise Information Systems (EIS). Such an evolving environment contributes to both the process and the system complexity which cannot be handled by the traditional architectures. The constant pressure of requirements for more data, more collaboration and more flexibility motivates us to discuss about the concept of Next Generation EIS (NG EIS) which is federated, omnipresent, model-driven, open, reconfigurable and aware. All these properties imply that the future enterprise system is inherently interoperable. This position paper presents the discussion that spans several research challenges of future interoperable enterprise systems, specialized from the existing general research priorities and directions of IFAC Technical Committee 5.3,1 namely: context-aware systems, semantic interoperability, cyber-physical systems, cloud-based systems and interoperability assessment.