Mass Rapid Transit (MRT) systems play a critical role in promoting sustainable development, particularly in megacities. This study assesses the quality of boarding/alighting facilities along with accessibility of MRT, as integrated system components which is vital for maintaining a safe, efficient and user-friendly transit system, in the context of built-up cities. A robust questionnaire form is designed using 29 selected variables derived from pilot survey which was administerd to 1,397 respondents across nine operational stations of MRT in Dhaka, a developing megacity of Southeast Asia. Using the collected data, Gini Index and ANOVA are employed for variable prioritization. Machine Learning Algorithms, i.e., Random Forest (RF) Classifier, Support Vector Machine (SVM) and Classification and Regression Trees (CART), are compared to assess predictive performance where RF demonstrated better performance based on accuracy. Additionally, feature selection identified critical factors related to MRT trip performance, such as switching cost comparison, feeder service cost, inclusive service performance, customer loyalty, lighting near stations, overall comfort, security. This study, further, incorporates two most crucial factor, switching cost comparison and feeder service cost to a hybrid function, assessing system components and user transferability, utilizing a novel matrix-based approach. The study’s conclusions provide insights into boarding/alighting facility and accessibility as system components incorporating hybrid cost function (HCF) to enhance the efficiency of MRT services in built-up cities across the world.