I also totally agree that a connection to a cloud storage is necessary! I use EndNote Web for my thesis as well as the iPad app and I wanted to download all my annotated papers to dropbox which was not possible… So I had to download one after one until I had all my papers - what a waste of time!
It would be perfect if one could link the references to the documents to alter the documents while annotating in the EndNote app.
Another thing regarding the annotations in the app (I know this does not fit in here!): A function to collapse the text to see only the annotated/highlighted parts, more options for note taking would be great (mind maps, etc.). The app LiquidText has several great functions that would perfectly complement EndNote for iPad!