The right comparison should include curriculum, recognition, total cost, assessment method, faculty support, practical learning and career services rather than looking at one feature alone. If your target role involves MCA vs MSc CS, include at least one demonstrable project rather than mentioning the topic only as a skill. This point is specifically relevant to the MCA vs MSc CS aspect of MCA study. For this specific question about MCA vs MSc CS, the practical takeaway is to relate the concept to your own MCA learning goal.