Choosing between Mechanical Engineering at MIT Manipal and ECE/CSE at MUJ depends largely on your choice,  goals, interests, and the future scope of each program. If you have a strong inclination towards understanding machines, systems design, and mechanical principles choosing  Mechanical Engineering at MIT Manipal would be a great option.

On the other hand, if you have interest in technology, software development, data analytics, or telecommunications then pursuing ECE or CSE at MUJ might be more suitable.

In the end , it depends on you that which field and career you want to pursue and not on the quality of colleges and their rating. Hope this resolves your query.