I haven't owned it for more than 24 hours yet, but an iPad with the Good Reader app might work well for you. Reads PDFs like a dream and does let you mark them up and export them as well. I imagine you could overcome the usb issue (something that bugs me as well) by using Dropbox or something similar.
Sorry that I can't give you more thorough info. Got mine (first generation) at the Verizon blowout yesterday. That was the first app I bought (and I only plan to use it for reading PDFs). But I was very impressed how well it handled them.
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