If Apple had provided a way to organize PDFs, ebooks, and other data files with some kind of database, I would love that, and I think it would satisfy most people asking for a file system. However, Apple has provided nothing. No file system, database, nothing.
As for Good Reader, I never really used the iPhone version, but I'm sure the iPad version is easier to use simply due to more screen space. It's hard to tell wether or not it'll work for you, since I don't know exactly what you found clunky about the iPhone version, but it's only 99 cents, and I think it's definitely worth a try.
In theory I like the idea of using libraries/databases instead of a file system a lot. I want my computer to help me organise my data and not have to rely on a simple, fixed hierarchy of folders. However it does sound like the iPad implementation is currently pretty half-baked. Until you can easily pass items between the libraries of Apps I don't think people are going to be satisfied.