Actually, syncing annotaded PDF is the solution I use, testing ezPDF Reder and RepliGo Reader (the latter seems to me a bit better).
The syncing takes place with Dropbox, via Dropsync
The issue there is how to keep the Calibre dir structure - that is how to export the library to the device the first time, in order not to lose all the metadata. Once the library is exported, with all the information, any change in the pdf files as such will be reflected either side when sync is performed
I opened a thread on this subject here
The problem arises when it comes to sync the annotations on EPUB books... they are not stored inside the epub file, thus making useless any sync arrangements
Does anyone have any clue on that?