BITS Pilani is located in Rajasthan, which is and used to be a part of India's so-called active north. As a result, BIT Mesra is not preferred by the people of the north, who have better options of IITs and NITs. While some go for the south. It is only an ideal place for Bihar, Bengal, Orisha, Jharkhand, and the neighboring state.
BIT Mesra was ranked 7th by India Today Group Survey, but it remains isolated in terms of fame because students are the biggest marketer for a deemed institution. If you say, “Hey, I am from Bit Mesra,” the likely answer would be, “Is it a subsidiary unit of Bits Pilani?” As BITS Pilani is more reputed.
Here are a few other reasons why BIT Mesra has not gained much recognition among the students.
This all that I have learned through my connections at the institutes. Hope this helps in clearing your doubts.