I don't think there is another brand with the same customisation ability as the Pocketbooks, certainly not in the big name brands who run their own bookstores.
As far as Kobo is concerned, these hacking threads may may be of interest because they do allow organisation by folder rather than the tagging systems favoured by the big names.
Adding alternative readers to Kobo devices
Koreader running on Kobos (all of them, hopefully!)
Cool Reader for Kobo
Android on Kobo: "Tips and Apps"
If you have detailed questions you'd probably be better asking them in those threads where the hack users/creators hang out.