OS X Mavericks finally brought iBooks to the Mac, but it only solved half the puzzle. iBooks cannot sync non-purchased files (PDFs, ePubs, etc) without using a cable and iTunes on a Mac/PC. Apps like Documents by Readdle and PDFpen by Smile Software have figured this out. Both apps can either sync via Dropbox or (gasp) iCloud. Why are third party PDF and document apps doing what iBooks should be doing? I know that iBooks is primarily for content purchased from the iBookstore, but what is the workflow here for iOS users if one doesn't use a third party app? There is no Preview.app for iOS. There is no built in way to sync PDFs (or non iBooks ePubs) without syncing through iTunes. It's very possible that customers in the future will be iOS only users (iPad + iPhone) and Apple needs to address this workflow issue.
Here is a legitimate question on the Apple discussion forums: Where Can I Save PDF Files In iCloud? Stop and think about all the awesome things a stock iOS device can do and then think about the fact that syncing PDF files without a Mac/PC or without a third party app isn't possible. A PDF added to iBooks on the iPhone (from a website or email attachment) should be synced automatically (over iCloud) to iBooks on an iPad and a Mac.
It appears we still have some low hanging fruit for iOS 8.