Both are excellent institutions, but the experience will differ between the two. Whereas IISc is much larger and has a more vibrant student community, the smaller batches in JNCASR allow for more attention and a better chance of getting into at least one of their preferred labs.

IISC is smack dab in the middle of a commercial area (well, actually, the commercial areas grew around IISc, but let's not get into that). JNCASR is less centrally located and more of a sleepy campus. It's a completely different story after the second year when the pressure is intense and lab work can be extremely demanding. 

There are no holidays for students (not even Sundays or national holidays like the 15th of August or the 26th of January, but there is a flag hoisting event so you get off work for at least an hour) and most P.I.s do not allow paid leave of more than two weeks per year. This is not to say that there isn't any fun on campus. Most of the rules governing on-campus life are lax, and the guards and staff are laid-back and don't make a fuss when asked to overlook a few things.