Certainly a matter of preference. For me, Calibre organizes books exactly the way I would if I was doing it by hand, so I love that it does this. But obviously it's all a matter of preference and how you use the tool.

If you use Calibre purely for conversion and delivery to your device and manage your library separately, you can always use the ebook-convert and ebook-device command-line tools, which are pretty easy use.