Calibre's interface isn't to my liking but since they added the possibility to manage collections/bookshelves ~two years ago for my almost ten year old kobo I love it a lot ^^. Managing collections/bookshelves on the Kobo is a major PITA.
Added support for Kobo's "series" organization feature as well. Apparently requires some janky 2-stage process because it's not done with the book's built-in metadata; you have to sync the books to the Kobo, then sync again for it to poke the special series sauce after the files are on the device.
Seems like a needlessly complicated way to do it when the books have series metadata, so props to Calibre for the extra work to support that!
Check out koreader for Kobo devices. I've been using it for a quite some time and it adds some nice Calibre features such as wireless sync. Besides that the PDF support is leaps ahead of stock Kobo
