In the end, it really comes down to the ecosystem you want to buy into. B&N or Amazon? Me, I'll take Amazon. And I like the Kindle design better...tried a Nook Simple Touch at Best Buy and didn't really like the heft or the hard-to-press page turn buttons.
Plus I am already well into the Amazon ecosystem
I know epub support is a huge deal for some people but I just don't get it. I'm perfectly happy with mobi format. I've never been in the middle of reading a book and thought "damn, i wish you were epub so I could buy you for the same price from store A instead of store B!!"
I'm perfectly happy to get my books from Amazon (thanks to Apple and Agency pricing there isn't really comparison shoppping anyway) and Baen.
I will be interested in the comparisons between the new Nook firmware update and the Kindle Touch. Amazon also advertises that they use a custom font and formatting to make text look crisper so who knows.