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.
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