+1 for Paper, but how are you embedding PDF? I can only add it if it's already in my Dropbox, and it is not editable (notes, highlighting, etc..) Only thing missing for me to make it go from good to great.
PDF has to in the dropbox folder somewhere before you can add it. Then it appears as a single page preview. Clicking on it allows to view the full doc within Paper, but there is no annotation feature as of now. Example:
https://paper.dropbox.com/doc/Demo-of-Paper--AHs_Q3BsPSNjYAO...