Paratransit systems are designed to cater to individuals with reduced mobility, and have played a pivotal role in providing essential mobility and accessibility for those who often encounter challenges with conventional public transport. These systems rely on flexible transport, and are characterised by their high configurability and uncertainty stemming from factors such as low demand, complexity, and the specific mobility needs of the targeted group. Unfortunately, some of these systems have encountered failures due to structural and parameterisation errors. This paper proposes a Decision Support System (DSS) to support the strategic and tactical decisions of conception and design of paratransit systems, as well as to support operational management. This system aims to integrate the interests of different stakeholders during the decision-making process in order to obtain more robust solutions. Particular focus is given to a segment of the DSS that interfaces with operational management and simulation components. This integration facilitates the assessment and comparison of alternative scenarios, utilizing diverse criteria to achieve the most suitable parameterisation and comprehend the associated risks tied to specific decisions. The tool provides assistance across various decision-making scenarios, and within this context, we will scrutinize its efficacy in identifying and comprehending the impacts of varying time window sizes on the systems' performance. The outcomes of these analyses underscore the significance of contemplating diverse parameters in decisions related to mobility. The tool provides valuable insights, enabling better alignment with genuine needs, and ensuring that devised solutions align with user preferences.