FISAT is just a private engineering college whereas CUSAT is one of the best universities in Kerala which means you'll have many opportunities at CUSAT. 

The table shows a brief overview of the institutions.

Discussed below are some of the reasons why you should choose CUSAT SOE (Mechanical Engineering).

Admission: (Winning Institution - CUSAT)

The admission process for CUSAT is different and requires clearing their own entrance examination while FISAT admissions are through the Kerala entrance examinations.

Other Factors: (Winning Institution - CUSAT)

• CUSAT is a tier 1 college. It is known even outside Kerala. 
• CUSAT receives higher funding from the central Govt. due to various accreditation.
• Many students from north India take admission to CUSAT. Due to this reason, CUSAT has a diverse environment. 
• CUSAT has a tough syllabus as compared to other universities but it is designed to meet the needs of the students and has its own perks.
• CUSAT was selected to be converted to IIT and an IIEST after, it didn’t happen due to some state political issues. However, this fact indicates that the college offers that level of quality education. 
• The faculty for Mechanical Engineering at CUSAT is quite diverse and you will have many career opportunities at the institute.

The only reason to choose FISAT over CUSAT should be only if you are restricting yourself to private institutes. Otherwise, CUSAT SOE (Mechanical Engineering) is a far better alternative.