I met a Nook engineer once, and she was convinced that the Nook was a better product than the Kindle. It's too bad that it never took off (as far as I can tell).
I think Amazon's software is better, though. More responsive. Better rendering of the actual book text (margins, line-height, font size adjustments, etc). Not to mention how easy they make it to buy books right on the device. And the books are usually a little cheaper on the Kindle store. Plus Amazon has tons of Kindle-exclusive content, plus they have extra hooks for Prime members, like the Kindle Owner's Lending Library.
This is another example of technical superiority not being enough to win (see VHS vs Betamax as the classic example but there are a TON of these).
I found this article by Amir Hirsch to be a good reference point for products in general, not just startups: http://fpgacomputing.blogspot.com/2013/11/the-stanford-start...
For some part of the market I think this was actually a strength, though perhaps not a big enough strength, or not exploited well enough. We got my uncle (American, aged mid-80s) a Nook for Christmas 2012, in large part because we knew he could go to his local B&N to buy books and have them loaded onto it. That's worked pretty well: he basically buys books like he used to, except now they are more portable and he can zoom in to compensate for his poor eyesight, which is easier than reading paper books with a magnifying glass. With the Kindle we weren't sure whether he'd enjoy having to figure out how to shop online at Amazon. He rarely uses computers, and even more rarely uses the internet, so probably wouldn't buy books from a desktop connection. So he'd have to buy them online from within the Kindle itself with no local customer support available, which even to me seems like a confusing interface (it's not quite as bad as trying to navigate Google Play on a smartphone, but it's not great).
I do appreciate your point though and I think it's just another example of B&N having poor marketing.