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I like Calibre. It's a bit daunting for a newbie due to there being so many features and so much that can be configured and changed and a lot of menu structure devoted just to that. Tutorials from helpful souls do help compensate. The database structure was chosen for good reasons as pointed out. Pretty obvious to anyone who sat down for a bit and thought about creating such a thing and what happens when references to imported books change if you easily allow for manual editing of storage and all the error handling required to keep up... Frankly, once the books are imported, you can do pretty much anything you like as far as creating shelves or collections.
I don't think the interface or look is bad. I do think a few things should be revisited like how one builds parsing expressions and the like to simplify the process. A GUI approach where one selects elements or common expressions from lists or inputs new expressions would make the whole thing a lot simpler than trying to remember which operator does what, if you don't often have need to build custom new ones, and would help people to remember by looking at examples as they go...
Overall, it is a killer program. I wish they had an Android version so I could maintain the full capabilities on my Tablet and dump reworked content to my ereader when away from home, but I guess my convertable laptop isn't really that much heavier.
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