Hate how it wants to copy and RENAME all the files
I stopped using Calibre because it insisted on copying and renaming the ebooks, except when it decided not to because there was already a copy in another format and it decided that it would be better to let Calibre repeat the conversion from the first copy it came across rather than, say, ask or find out which copy had the best quality.
I have the ebooks already sorted into directories that group them by purchase - a lot of Humble Bundles, for example - and it makes it nice and easy then to check things like "are there any items I've not yet downloaded from Humble?" when even the really lazy way works (kick off the downloads but click "no" when told the file already exists and do I want to overwrite it).
Other files have names that were changed when downloaded, usually to keep the numeric file id from the original source (downloaded hardware manuals, research papers, LEGO build instructions etc) but tack on some more meaningful info as well (LEGO set number - not the same as the file id - set name, booklet number x of y; or subject matter, main authors, year published, which proceedings). All really useful info when the file is sitting on an SD card to go into one of the ereaders. Most of which is lost when you let Calibre get its hands on the file. Or some weirdness means every paper is renamed "1980 Proceedings on Ferret Wrangling" so they are all copies of the same thing and only one need be kept.
I can see Calibre working well if you are happy to let it take over your files or you are happy to just keep two copies of everything. Maybe I'll just buy enough file server drives that the duplication seems acceptable.
Or, best of all, you will all chime in and point out that Calibre has had a "leave my files alone" flag for years now.