I had a Nook Classic for a while, and it was good for shelves and all, but I went to the STR for the better screen and longer battery life.
Got those things, but everything else was not so great.. If you have a big library adding books to the shelves you create is a laborious process, but you already know that from looking at your mom's reader. In the end I ended up giving my STR to my own mother. I made sure it was good and organized but that took more work to do than I ever want to again on a library.
If you want good organization I'd say go with the Sony's PRS-T2. You can find one for about a hundred dollars in Best Buy sometimes. With Calibre you take your books, making sure they are still in EPUB format, lump them in the series columns with names like-Brooks, Terry (Sword of Shannara Series)-and sideload the books into the Reader. It will become a collection you can access immediately without having manually create it on the Reader. Best part is if you do multiple shelves the Reader will even slot them in alphabetically.
As for stripping DRM there is a place on the internet suggests ways to do it. Hint-old show starring a furry brown alien. Think of him as an apprentice of sorts.
Still I really do recommend the T2. No rooting necessary. I have 4k books in my library now, and with Calibre I was able to load all of it into the Reader divided up into about 450 collections. Even better is that I bought my wife the same reader, purchased a memory card for it, cloned my memory card onto the new one, and loaded it into her Reader. Instant Library Duplication with no extra work.
The Nook STR is a great reader, but the ability to manage collections or shelves from a computer was what really sold it for me on the Sony. Your mother's frustration about the Nook's shelving system is not unique. With no 'Add to Shelf' feature paging through your entire library to add one book becomes a nightmare.