if goodreader handled epub documents i would be using it right now. since it doesn't i can only use it for pdf files. and i do have a folder structure implemented in goodreader to organize those documents.
i look at a cover for all of 5 seconds, i spend most of my time reading the actual document or book. pretty covers on the shelf don't interest me as much as what's inside. when i am looking for a reference book i want to find that book fast, i generally know what title i'm looking for. it is far easier for me to scroll an alphabetical list of titles than hunt through a list of 1.5"x1" cover images looking for whatever animal graces the cover of an o'reilly book i need. and as i said i have many white papers and technical documents that have no more than a few words on a page as their cover page. they have no pretty cover to even look at. calibre creates a book cover for them that is a scaled down version of this page, they would near impossible to distinguish one from the other in iBook's shelf view.
go and download a bunch of free books in the iBook store and get those generic brown covers with small text title. now swap over to list view and look at those same titles in larger text which can be sorted by title, author, category or searched through using the search box up top. which view is more useful for picking one book you want out of hundreds?
sure, if apple gave iBooks some sort of folder structure, or the ability to create additional book shelves, it would easier to organize, but they didn't, and i'm not scrolling through a 10,000' high bookshelf to look for one cover out of hundreds.
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