With the sony you are not tied to one store, you can buy from any store that sells epub (B&N excepted for the moment), so theoretically you have more choice. On the other hand, amazon has a very good and diverse collection (or so I've heard), and most of the time better prices (again, this might change in the future).
What I would do in your place, is search for books I would be likely to buy for my future reader, and check the availability and price on amazon and a selection of epub stores (not just sony). You can use websites like
http://ebookprice.info or
http://inkmesh.com to help you with your searches, but don't take the information they give you for granted, I hear their databases are not always updated.