I hae used ebay (when the India site still existed), Amazon, Flipkart and multitude of other sites for online purchases based on deals offered. My three criteria for choosing a site are
1. Access to customer service (I try calling up their customer service number before ordering)
2. Money back guarantee (Some sites offer them)
3. Deal available on the product
Flipkart was at the top in India until Amazon came, and now Amazon is Flipkart a tough fight and is growing at a much faster rate in India both in terms of popularity and sales. Here I think both these companies are good at quality and service but I think overall Amazon.in has a bit of edge in every department.
I prefer Amazon due the large inventory of books that they Keep. My first introduction to ecommerce was way back in 2013 when i ordered a chemistry book for IITJEE from flipkart but they didn't focus on their educational books category which led me to amazon. Amazon has tons of offers on all kind of preparatory books and last year they even started dedicated pages for different exams with faqs info etc. Till now I have bought more than 20 books from Amazon along with other stuffs like mobile phone, microphone, etc.