I have the major part of my library on my Android device, and access it without using calibre at all.
I just use calibre to fix new books and save them to a shared directory tree on my NAS. Then I sync this tree to a folder on my Xoom. I think I have around 6 000 books there, mostly epub and a few pdf. I then only access the books from my reader app, Mantano.
The sync is done from my Xoom, automatically every hour, if the Xoom is charging. If I had other devices I wanted to have the books on, I could sync them the same way.
The tree is organized by genre and/or type of publication. But once the books are imported to Mantano I can access them by Author, title, series, folder, tags, format, dates, read/unread and whatever. Almost as flexible as calibre...
I keep all the books in calibre as well, but that is just as a backup. And to allow me to quickly check so I don't buy a book I already have.
So I don't really use calibre to handle my books. I just use calibre to prepare them an make them available to my reading device.
I spend a few minutes in calibre for every new book I get, but other than that almost nothing.
There are a few programs for collections, with adaptions to handle books. You could try them. And use calibre only for conversions and so on. Just google "ebook collection software" or something similar.
That said, the problem isn't calibre. It's you. You have fallen prey to a mental block and are unable to see how much better everything would become if you think of the calibre library tree as a black box without any way to look inside it. Most of the calibre users comes from there, but most have been able to break that mental block.