ISI, at the undergraduate level, teaches statistics and mathematics and IISER is in charge of General Sciences and MNNIT Allahabad offers engineering programs. Think thoroughly about what you want to pursue because the paradigms are different and the impact on the industry is also different.
If you go for civil engineering at MNNIT Allahabad you will find that the subjects are similar in the first year. You can top your class if you study hard. Only the top 2-3 students get the opportunity for changing their discipline after completing the first year. Changing your discipline will enhance your eligibility to the other institutes you have mentioned in your postgraduate.
ISI gives you five options at the postgraduate level:
IISc offers a number of specializations in engineering and general sciences. The eligibility, however, was restricted to undergraduates and the disciplines related to them. For shifting disciplines, you will have to appear for the GATE exams for the discipline you are converting to.
My friend appeared for his GATE exam in CSE to pursue the same in M.Tech. ISI is unique in this case because there are no restrictions here.