calibre

I fully agree with you! I spent a lot of time to THINK about the best way to organize books even before using any e-book management software. I concluded that due to the following reasons:

1. Lack of dedicated ISBN number filed in metadata in official standards for all the popular e-book file formats (PDF, CHM, DJVU, EPUB) I am forced to use file name as a ISBN storage. If popular e-book file formats did have dedicated ISBN number in that case ISBN number for my e-books would be inserted into book files (and then extracted easily with any e-book management software) and in that case I wouldn't care if Calibre or any other e-book management software insists on its own naming scheme. The essential point here is -> I cannot trust a buggy SW to control the connection between file names and ISBN numbers for my book collections!

2. Performance hit when Calibre accepts a large number of new books (e.g. >100). Since Calibre insists on controlling book files it hits performance wall when it has to ask operating system's File System to check for name collisions for every file and directory created. I am using another e-book management software which does not care how the file will be named (in fact it relies on the fact that the book files already exist somewhere so there is no performance hit). Importing 500 book files in Calibre is extremely SLOW especially if your e-book collection is large. On the other hand importing 500 books in the SW I am using right now is almost instantly (however that SW is poor in search capabilities which is a strong feature of Calibre).

Normally I would use Calibre but due to its deep reliance on its file/folder naming control (which is deeply rooted in its architecture) I am forced to use a weaker SW... Too bad!

You just have to accept that the manager, manages your ebook collection for you. That's it. Simple!

I would not say Calibre is useless! It is the BEST ebook software out there. If you don't like it, you don't like any of them.
You can always manage your ebooks manually however you like, but Calibre HAS to have its own libraries in order to store the metadata, sort books into folders, by author, etc. It's also very useful because you can search for a book by title or part of one, author, or part of an author's name, rating, etc. This would not be possible (or at best extremely slow) if you used your own folder system. It DOES sort all books into folders by author! They're readily accessible through your computer's File Manager, as well, if you want to find a book the hard way. I've done this using Thunar (which isn't available on Windows, for those of you thinking you could use a better file manager than the horrible one provided by MicroSoft.)
AS to ISBN number, it CAN download that metadata from the web and insert it. It's not automatic because there are different sources, and you choose the best match. Otherwise you might get the WRONG metadata for a book titled
"Ocean" By "Waves" or something.
You can have multiple libraries. You can name them "Fiction" and "Education" and switch between them, in your example.
If you do decide to modify the Calibre Libraries manually (say, adding a book, or modifying a book, or deleting a book) you will most likely ruin the databases for the metadata, number of books, etc. Instead, clone the library to another partition or drive and do your modifications there! Also, if you do manage the content of your Ebook reader manually you're doing it the slow, hard way, unless you have one with that capacity built in, such as Kindle (in which case, USE THE KINDLE software if you're happy with it.)
On Android devices I sorely miss the full-blown Calibre. There are no good alternatives to it for this OS. They all require you to manually sort your book collection, which is difficult to even find in the Android file system and its persnickety icon based interface with all those slide and tap and touch the screen things (shudder)! I'd prefer an automatic Library where, when you open your Calibre application, you could sort your books, etc. as in the full Linux edition (and I suppose there's one for you few remaining Windows users, as well.) One day we'll have Android with NO ICONS and NO TOUCHSCREEN needed, I hope. Ubuntu almost had a solution...
Calibre CAN modify original files, saving the originals. With this feature, you can convert books to other formats, MOBI to EPUB, etc, and you can optimize them for whichever reading device you prefer, Kindle, Nook, Kobo, etc. You can even modify an EPUB that has no chapter structure, and add a table of contents, if you want. You can edit a book with a lot of typos in it to correct them.
As to others objections to its "clunky" look, YOU CAN MODIFY the interface however you like, removing icons/shortcuts you don't use, selecting wide or narrow screen format, etc.
Yes, it CAN be slow if you try to add 100 books to an ereader device (also not recommended.) That's not Calibre, that's the DEVICE speed holding you back!
If Calibre were slow in moving books, when you clone a library of 100 or even 500 books with it, it's almost instantaneous. I've done it. You COULD also do this using File Manager on your Linux based computer, of course. (I don't think you can do it with Windows, which is one of its many flaws.)