Model-Based System Engineering (MBSE) is a popular mathematical and visual approach to the design of complex control, signal processing, and communication systems. It is used in safety critical industrial domains including aerospace, automotive, transportation, medical and robotics applications. Our group develops methods and tools for model-based system reliability and safety analysis with the main focuses on stochastic modelling of error propagation processes. This article is devoted to the optimisation and extensions to our analytical toolset. We have investigated the key modeling paradigms, requirements and industrial needs and have formulated the list of particular extensions.