I also had an extensive collection of epub books which ruled out Kindle. My early experience with Nook almost led to a return before I found softrooting. I looked at the new B&B shelf update and gave up when I found out I would have to add each book, one at a time, using their keypad. Nook has no interest in really supporting sideloading at all.
I switched most of my reading to the Jetbook where sorting is simply a matter of moving books to folder. Gee B&N, how hard would that be???
My advice would be to only go to Nook if you are confident that you can softroot. Without that, you will be frustrated beyond belief.