Smart transportation network development with environmental issues into consideration has brought Industry 4.0 based solutions on priority. In this direction, battery-powered electric bus systems have been considered widely for ensuring flexibility, operation cost, and lesser pollutants emission. Industry 4.0 provides automation through a cyber-physical system (CPS), the interconnection of bus system entities with industrial internet-of-things (IIoT), remote information availability through cloud computing and scientific disciplines (human-computer interaction, artificial intelligence, machine learning etc.) integration. In this work, a discrete event-based simulation-optimization approach is integrated that take care of bus energy consumption according to real-time city's passenger needs and on-road friction levels. The proposed simulation optimization methodology utilizes multi-objective with dependent and independent variables for optimizing the overall system performance. In simulation optimization, objective functions are designed to tackle battery consumption, Internet-of-Thing (IoT) network performance, cloud operations efficiency and smart scientific discipline integration. Simulation parameters are based on a real-time bus system which is further analyzed, filtered and adapted as per the needs of the system. In another analysis, supercharger's capacities are varied to evaluate the performance of the proposed system and identify the low cost and efficient smart transportation system. Simulation results show different scenarios for variations in the number of buses, charging stations, bus-depots, mobile charging facilities, and bus-schedules. Simulation results show that the average passenger's waiting time in the waiting is (after ticket booking) varies between 0.2 minutes to 0.7 minutes in real-time traffic conditions. In similar traffic conditions, total passenger's time in system (ticket booking to travel) varies between 41.6 minutes (for 24 hours) to 45.5 minutes (for 1 year). In the simulation, priorities are given to those dependent and independent variables which save the battery consumption and elongate the utilization of buses. Lastly, it is also observed that the proposed system is suitable for resource-constraint devices because Gate Equivalent (GE) calculation shows that the proposed system can be implemented between 1986 GEs (communicational cost without confidentiality and authentication) and 7939 GEs (computational cost with HMAC for authentication in data storage). This ensures varies security primitivs such as confidentiality, availability and authentication.