Dear Aspirant,
It is not fair to compare different courses of two colleges to get an unbiased answer.
Let me put down a few facts.
1. MIT Manipal is an older and more reputed campus and hence you will get better alumni network, faculty support, exposure for internships and jobs etc. If you choose ECE and are looking for a career in Software then this is a better option. You will have to work hard to maintain your GPA above 8 and also to learn the programming via internships, and extra courses.
2. MIT is better than Amrita as the campus is better and they rules aren't strict hence you'll get opportunity to grow as a person as well.
3. The MIT Manipal tag will help you hence if you are looking for a good opportunity and are willing to work hard choose it.
Hope this helps.
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