To improve the Information Technology (I.T.) graduate skill set, students need to be immersed in as realistic a software development environment as possible. In continuing our work on integrating Agile Methodology into the Capstone Program of our Bachelor of Science in I.T. (BSIT) degree program, this paper discusses the student challenges and difficulties during the software development project, and provides recommendations on improving the student overall learning process in such a program. We collected survey data from the whole population of 90 BSIT students across four academic years about their experience with their client and the Capstone Program itself. Conceptual content analysis was then applied to discover and describe underlying themes. Also, faculty advisers were tasked with writing about their interactions, thoughts, and observations on their respective student group advisees. These showed issues with time management, communication, and competency. Also, groups that excelled exhibited better team coordination and a complete grasp of the Agile methodology. For future implementations, clearer task definition and reducing the skill gaps are necessary for better execution.
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