First of all thanks for A2A.
Now coming on to your question, MUJ being the new university and a part of Manipal Group will be one of the top universities in India but that will take time. Apart from that MUJ having the best hostels facilities and the hostels are rated 4 stars and one of the best hostels in the country but with some restrictions on the timings (7:30 p.m in timings for both boys and girls). But they opened restaurants ,food courts,juice corner within the campus so that won’t be a question to bother about.
And now coming on to the best branch then I would suggest you to go for CSE as this is the only branch Having ample opportunities with in the campus and off campus as well.