JNU conducts the toughest entrance for MCA. Its faculty and environment are ideal for this degree. MNNIT Allahabad is a good institute, but its MCA is not comparable to JNU.
However, JNU does not have a concrete curriculum for its MCA entrance. Its entrance is conducted in a non serious manner, and the paper is difficult to crack. Moreover, it has a lot of reservations and quotas, even on such limited seats.
On the other hand, NIMCET is conducted in an organized manner, and its paper is easy to understand. The syllabus and blueprints are made available on the official website for good preparation.
Despite all this, JNU has a very professional education system. It does not offer any placements, but you’ll get good exposure on campus and land a job on your own. The MCA faculty is highly experienced, but I am not well aware of the university’s infrastructure.
Talking of MNNIT Allahabad, it is a highly reputed NIT with a good placement record. Its campus is completely ragging free, and the environment is strict on academics. But its hostels aren’t in a good shape.
I would suggest JNU New Delhi for an MCA, but even MNNIT is a decent choice.