MCA Fees

If you are looking at doing Masters or PG, CUSAT is definitely better that CET. I work very closely with Academics and personally believe that academic freedom to design courseware for the quality of their students is something that is needed to impart good quality education. CUSAT has this with some very well educated professors who are dedicated to train students well. The govt is also pumping money to improve the facilities here. In case of CET, it is tied to the KTU syllabus, under which even the worst colleges in Kerala will be affiliated to. As a student, you will be offered the same course in CET which will be offered to those type of colleges.
Also, with CET, your Prof might just get transferred by the government, which will never happen with CUSAT. This should be a major add on point for CUSAT.
Having said, all of this, if you are looking at B.Tech, when I took admission is 2010, CET was better than CUSAT School of Engineering(which offers the Bachelors courses), both in terms of placements and quality of education; there are a lot of contract faculties in CUSAT SOE. With the KTU structure into place, I am sure CUSAT SOE will definitely improve in the coming years and whereas CETs quality will come down, if it doesn't become autonomous.