I agree too.
Let me give you one example: WebOffline is an app you can use to store an entire website locally on your iPad, so you can view it even without an internet connection. A website consists of text (html) files and images (jpeg). Both can be read by GoodReader, but GoodReader simply does not know anything about any stored website in WebOffline. For the same reason, GoodReader also can't send any file to WebOffline.
That means you can not -at least not completely- sync two iPads this way.
Johan W. Elzenga, Editor/Photographer