Airline and train operations are feasible thanks to the Command and Control systems which involve interactions between human operators, technology, and procedures. In view of the expected growing demand, significant changes in these C2 systems are in development in many countries. Such changes can lead to both positive and negative emergent behaviours. One of the promising approaches to capture this behaviour is agent-based modelling. In order to develop and implement a generic agent-based model for C2 systems, this paper compares and evaluates two C2 systems from the railway and airline domains. The paper conducts a systemic agent-based analysis that explores various dimensions including organizational structure; agents characteristics; operational uncertainties and workflows.