My biggest gripe with calibre is search. If you're used to Google, Bing or Spotlight search results, calibre's search feels like you're stuck in early 2000s.
Here's an example. Say you're searching for "author - title". See that hyphen? Well, unless your book has a hyphen in it, Calibre won't find it. It also won't find it if you put a colon and colon doesn't appear in the title. Something like "Title: Subtitle". Today I was searching for a book and couldn’t find it because I used a hyphen. I found it through Spotlight instead.
Another issue is stemming. Calibre still can't can't return search result for "network" if you type in "networks".
http://stackoverflow.com/questions/9...in-python-list
All of these issues are becoming more pronounced as Calibre is moving towards being more monolithic so using other tools is becoming problematic. Before, you could just do a grep/find or Spotlight search on calibre folder and find the title/author easily but now with super-short filenames, that becomes impossible for books with longer titles. Calibre's philosophy is that you should not look into Calibre Library's folder but that means that search should be as good as or better than what the OS provides.
Unless you can easily find things through Calibre's search, using libraries with large number of books is becoming problematic (to me anyway).