You will have to do every good thing that the others existing(amazon, B&N, Flipkart) already are doing. Like the extensive collection of books, the quick delivery, discounts, sales and what not!

Those apart, I guess the most important aspects to address would be,

1) What to do intend to do different from the currently existing ones?

Most online Bookstores thriving today have something unique. Great discounts, free shipping, or some of them cater to a particular customer set like students, or the scientific community and the alike. So, you will have to stand out and get noticed.

2) Are your target customers new to the idea?

An example would be Flipkart in India. Flipkart pioneered in India what Amazon had across the western world. So, by being the first in the country, you would have an advantage. Now, if you were to open a online bookstore in India, you will have to compete with the likes of Flipkart and a few others.

3) Technology!

Everything today is driven by technology. Tablet sales are rapidly increasing. People are open and accepting the idea of reading soft-copies of their favorite novels on tablets and e-book readers. So, your store will most likely have to have a e-alternate to most books so that people using a tablet or a e-book reader will be potential customers too. You may also want to build/design your own tablet/e-book reader and lock down people to your eco-system like the Kindle and the Nook.

Will add more, if anything comes up! :)