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I think the thing to realize is, Calibre seems to be designed with the idea that it is your repository for books and not simply a tool to modify information in an existing repository. It is very similar to the concept used by iTunes (depending on your iTunes library settings of course), where you import your file(s) into the tool and after that you let the tool handle every other operation (editing, conversion, file transfer, etc). Therefore, if your only goal is to change meta data and not use any other feature that Calibre offers, it is a rather poor choice because of the reasons mentioned by other posters (tedious process flow of import file->change data->export file). If, on the other hand, you need to convert the book or edit the metadata of multiple books at once, it might make more sense.
As far as using Calibre as the actual repository, I personally think it leaves a lot to be desired when compared to iTunes or my own file structure archiving system. That being said, I'm sure others love it and it fits their needs/tastes perfectly for that task.
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