For me, the whole point of having Endnote on the iPad is so that I can carry my PDFs around with me. I strongly feel that all attachments should automatically sync to the iPad. In fact, I have to confess that I am not imaginative enough to figure out why one would want Endnote on their iPad without the attachments, particularly since there is no Cite-While-You-Write functionality on the iPad (and I don’t miss that-I use LaTeX).
As others have mentioned, I also think it’s important that the annotations not be iPad-specific. And I will add another vote for SugarSync integration.