Both institutes are relatively new and enjoy a similar status and brand value in the education world. IIT Palakkad is a new IIT while IIT Dhanbad although an old institution has recently been given the IIT title. So that leaves us with preference as the major factor in determining which institute is the right one for you.
MNC is a blend of both Math and Computing concepts and is often very rigorous. The mathematical proofs and theorems form a major part of the curriculum and CS comprises just a minor portion of it. Unless you are a math lover or are genuinely interested in it, this branch might be very challenging for you as the concepts are very advanced and nothing like what you studied before. CSE on the other hand is an evergreen branch with broad prospects.
Moreover, the faculty of IIT Palakkad are from IITM also thus improving the quality of education offered. The infrastructure is excellent with great accommodation facilities.
Definitely, this is not true. Though IIT-Palakkad is doing good and showing decent growth, it can't be ahead of the old and well-established IITs. Here are the best IITs in terms of different factors.
Academics & Research - IIT Hyderabad:
IIT Hyderabad has tie-ups with Japanese universities and companies. The fractal academic system, innovative curriculum, great faculty, and locational advantage of the institute results in a good placement. It is undoubtedly one of the best IITs.
Alumni Network - IIT BHU:
BHU had a reputation of its own even before it was an IIT. It has a huge alumni network. You will get to meet IIT BHU alumni in top MNCs across the world.
Coding Culture - IIT Patna & IIT Indore:
IIT Patna and IIT Indore have been doing exceptionally well in competitive coding lately. Their performance in programming competitions, GSoC, and other similar events proves that.
Although IIT Palakkad is a decent IIT, it still has a long way to go, before it can be considered as one of the best.