It is disappointing that as Apple users we are used to doing things a certain way for years, and Apple's way forward results in less functionality and flexibility.
Here is a list of all the problems I have been facing with iBooks for Mac:
1. Transfer of Books to iPad or iPhone from iBooks is non-existant. If I create or download a DRM-free epub and or PDF and add it to iBooks for Mac (i.e. it wasn't downloaded from the iBooks Store), there is no direct way to transfer them to your iOS device through iBooks. Even books downloaded from the iBooks Store, since iBooks itself doesn't allow the transfer of files to the iOS device.
2. iBooks doesn't allow us to Edit metadata. Many PDFs come without metadata. And to organize them into the library as was previously possible in iTunes, we could add Author, Genre, Year, etc... Also even for books we actually download from the iBooks Store maybe we want to change the Genre or Category the book is in or simplify the Author's name.
3. iBooks essentially duplicates any PDF or ePub we drag to it into it's own library. Acting like iTunes "Copy files to iTunes Media Library when adding to library". If I have hundreds of PDF's that are hundreds of Megabytes in size, I don't want them duplicated again, especially when it's duplicated on my default Macintosh HD whom many people have as SSDs nowadays.
4. iBooks doesn't allow us to create or choose multiple libraries and have them in any destination we want (like it is possible with iTunes, iPhoto, Aperture, etc). By Option-Clicking on iBooks we should have that option.
5. The ability to delete Collections in iBooks for Mac.
All the above problems are surprising, as what essentially Apple has done is a book reader, and not a book library management tool. With books becoming more and more digital and more and more people using them, so does the amount of books in one's collection grow. It is virtually impossible to manage any book collection with such a lack of features.
Should anyone have solutions to the aformentioned problems or ideas on how to overcome them, please feel free to post them here.
Should anyone have other problems they encountered in this initial version of iBooks, please feel free to post them here, as this would be a good place to sythesize all that's bothering a lot of people with this new phase into Apple's ecosystem of iBooks.