IIT

1 PlacementsThe NITs you mentioned are a lot better than the new IITs for this field. The number of companies they attract are huge. The scope here is as good as the old IIT. Only minor difference that I can think of is the salary offered. A company offering 9 LPA in the old IITs may offer 8 LPA (for the same profile) here.
2 Campus Life
Damn the new IITs. They don't even have their own campus yet. Either they have borrowed someone else's or they are arranging different activities at different places. Trust me you miss out on a lot of things that way. I have friends who have regretted their decisions.
3 Brand Value
Ask any recruiter in India, they will sure recognise the tags 'new-IIT' and IIT differently. After all you miss out on a lot of exposure in the new-ones. Ask anyone outside India, they know none, neither IIT nor NITs. The ones, who know, always hold the older institute at a higher level (truly so). I guess the IIT tag is not enough here unless you want it for your friends and relatives.
4 Branch Choice
If you really love a branch don't hesitate to choose it. But when it's between a 'good' (with good I mean high cut-off ones) branch in a new IIT and a decent one in an old IIT time and again the later has proved to be a better choice. These are facts I am stating here (faced by my friends). Tell you my story I didnt even apply for any new IIT. When it's between the same branch in new IIT and a top NIT, I would go for the 2nd option. (I was stuck with a 5yr branch in an old IIT and a branch of my choice in a top NIT, I chose the latter and I am pretty happy I did that).
5 Alumni
Older the institute stronger its Alumni power because this isn't what comes overnight.

For M.Sc, there is something called JAM exam.
You can get more information here:
http://jam.iitm.ac.in/jam2016/ac
The candidates who qualify JAM 2016 shall have to fulfil the following eligibility requirement (ER) for admissions in IISc and IITs. All candidates admitted through JAM should have a Bachelor's degree. At least 55% aggregate marks, without rounding off, (taking into account all subjects, including languages and subsidiaries, all years combined) for General/OBC-NCL category candidates and at least 50% aggregate marks, without rounding off, (taking into account all subjects, including languages and subsidiaries, all years combined) for SC/ST and PwD category candidates
in the qualifying degree. For candidates with letter grades/CGPA (instead of a percentage of marks), the equivalence in percentage of marks will be decided by the admitting institute (s).