Congrats on your Nook! I am sure you will love it.
One of the reasons I rooted my Nook was so I could have my docs and B&N books in the same folder. It also allows me to add tags so I can look up a genre or series, so I don't even use the shelves. I am not too worried about the warranty. I will just put it back to 1.5 if something goes wrong. Also, if you get a square trade extended warrenty, they don't care if it is rooted or not.