IISER would be a very good option if you are interested in pure sciences and I really think if you want BS you need not go abroad. IISER and IISC would be really good. Though you can go for PhD in any good country you like. As for the preparation, jee advanced preparation would be great as you will have enough time to prepare for it and might get iiser is you rank within 10,000. However, if you do choose to prepare only for jee main, you might get iisc bangalore (at a very high score though) and engineering as well.

Also, for iiser there are two more ways of getting in-

1. Kvpy (one of the most reputed scholarship examinations)- need to have good rank in it.
2. Scb (only top 1%of board students are allowed) - 50%of the seats at iiser are alloted through the IAT exam they conduct.

Hope you decide what's best for you!

All the best for the future!