Yeah, the file management and content loading is probably my biggest gripe with the iPad currently.
iTunes just isn't designed for managing different types of content. It's great (IMO) for music and podcasts--ok for Video from the iTunes store as well.
But it needs a major redesign to work with books, PDFs, word documents and all the other file types apps on the iPad can handle. And the iPad needs a central location for this content so all apps can find a file (say a PDF) vs. having to drag it into each apps file sharing location separately etc.
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