Waterstones managed to capture the bookshop atmosphere with their store design, but that's always been a bit of stick-on fake marketing.
Commercially they've always been the equivalent of box shifters. They define the mainstream, and they don't do much to support work outside it. In fact they've homogenised the market and made it harder, not easier, for indies and smaller authors.
Although having said that, if it's down to Tesco etc for paper pub and Amazon for the rest, that's obviously going to homogenise the market further.
I think this could be the year when publishing finally wakes up to the Internet and realises that except for the top 250 or so best-sellers, it's pretty much game over for paper - if not now, then certainly over the next few years.