I just got a new Kobo Touch yesterday but the shelves feature seemed broken by the fact that I couldn't do a "check all" while searching to add books.
So I wrote a python script that will build shelves based on the directory in which your ebooks are located. For example if you have all IronThrones books in the folder /mnt/onboard/IronThrones it will make a shelf named IronThrones with all books of this folder added.
The script is here http://pastebin.com/hX2kqQ9b
I don't have time to explain how to make it works, but I'm sure those having rooted their kobos will have no problem.