Comparing School of Engineering CUSAT and Jamia Millia Islamia is not suitable as both the colleges are well established and are holding their culture and curriculum really very well. So, choosing either of them would not be easy.

But, as far as I know, Jamia Millia Islamia was established 100 years ago and is better than SOE CUSAT.

Jamia Millia Islamia will offer you a productive and competitive environment. You will also get to do lots of extracurricular activities and will get to learn from highly efficient teaching staff in JMI.

In CUSAT, you might be taught by recently graduated teachers. This will not only affect the teaching methodology but a good exposure as well.

CUSAT is nicely harnessed and handled by various Political parties for their own benefit. You can see a few strikes now and then among students and parties. But it should not be your concern as you are going to study there and grow productively.