In a situation where you are getting lower branches at IITs and top branches at very new NITs or IIITs, I would suggest you to go with the former option. If you would have secured a rank enough to secure a seat at one of the top NITs in CSE ECE ME EE, only in that case must you overlook your JEE Advanced Rank for JEE Mains. Secondly newer IITs have relaxed criteria for Branch Sliding , and you can always upgrade your branch once in Institute. Secondly, in todays Industrial Boom, at IITs whatever branch you are from you always have options to pursue and nurture your software and analytics skills, register for a Minor Degree besides Major and bag a Non Core Sector Job like any other CSE Student, hence more opportunities, unlike newer NITs.

Since you are stating you will be eligible for IIT BBSR Civil, assuming you are from GEN Category, you will also be eligible for the following branches

IIT Roorkee Geological Technology

IIT KGP Mining Engineering

Material Science/Metallurgical

Mechanical Chemical Engineering

At some of the noted new IITs.

From my perception IIT Gandhinagar Civil or Material Science should be the best choice, provided you are interested in it. IITGN Material Science is leading Reasearch and Development in the field of MSE today in India next to IISc and top IITs. Every year more than 50 students from IITGN Civil, Mechanical, Chemical and Material Science Engineering move to US to pursue their Masters. Gujrat itself provides ample opportunities for career and placement prospects. Do give it a thought.

Of course if IIT Bhubaneshwar has a vicinity advantage for you, do choose between Civil or Metallurgical there besides considering ISM Dhanbad and IIT BHU, both of which are standard Old Technical Institutes and provide proper training and placements are are located on the booming Eastern Industrial Belt of India.

For more information and college prediction do follow the links below

https://engineering.careers360.com/jee-advanced-college-predictor?icn=QnA&ici=qna_answer