I would say that IISER Bhopal will always be a better choice than VIT Vellore. The primary reason being VIT Vellore is a private college and IISER is a reputed government college. If you plan to do masters then too the IISER tag will help you. I do not mean to say that VIT Vellore is not a good choice but comparing to IISER, VIT Vellore will be less preferred. IISER will be more beneficial if you want to pusue pure science.