BITS Pilani is more famous and has better industry recognition. It offers a lot of academic freedom to students. It follows a zero attendance rule policy. Due to the strict selection process, the peer group of the institute is excellent. You will be sharing your lectures with some of the sharpest minds in the country. Owing to better industry connect, students get better internship opportunities from BITS Pilani.
I have a few friends at both institutes so I can shed some light on this. Here are some of the points that differentiate BIT Mesra and BITS Pilani.
Differences:
So at last but not least I can suggest to you that Pilani is surely better on almost all counts.