Amazon has the biggest and most complete online store in USA and probably in the world. It is true that maybe there are a few titles that cannot be found in Amazon (had not happened to me yet) but that happens in B&N as well.
In a short, Kindle users are backed up by a solid and big company and that's always a plus.
Regarding the warranty, I actually advise you to buy in a brick store
Why? the device will be supported by Amazon anyway, but if there is a Best Buy or Target close to your home and the device failed, you just go back to the store and get a new one the same day. No waiting, nothing to ship, plain and simple. I also keep my original boxes and receipts for about 1 year. That helps a lot in case of potential issues.