My biggest problem with iTunes is that it is more difficult than most devices to move files back and forth. Cut and paste into the specific section for an app does not work on Windows as I would expect. Sometimes you can only drag from another window, which is not as easy when you have 2 large windows open.
I would prefer a straight file system, perhaps with folders for the different apps, instead of everything being "hidden" on the iPad/iPod Touch.
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