Guys, check this out
http://www.youtube.com/watch?v=j6nDbE1CK3o
The part with the PDF editing and so on is amazing. Just remember that iPad will be far more flexible than any of the other ebook readers on the market due to the App store. There'll be so many applications just for PDF to match what you need.
@Johannes,
http://itunes.apple.com/us/app/arxiv/id302515757?mt=8. It's the Arxiv client for the iPhone, you can contact the developer if he's doing the iPad version for it. If he's not, i'm sure somebody else can develop it for you if you ask around.