The absolute number on problem with pre 1.5 nooks was the crappy library system for side loaded books. If you don't already have many, many hundreds of books, starting from scratch with the "shelf" system is a half decent option, albeit without any decent search or sort options and no cover view. Keep in mind, you cannot set the shelves up in any way other than with your nook keyboard and a very ponderous bunch of transfers. It also doesn't have any directories or any way for Calibre to see what is going on.
So, as for library, the version from nookdev is clearly superior in every way but the B&N system fixes one problem. Keep in mind, Nook had a problem with more books than 1275 (sorting gets corrupted). I've heard that nookLibrary from nookdev tolerates around 2400 titles before it runs out of memory.
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