Good call! Indeed OneNote is a rather hidden gem.
There are a few concerns through... On 2007 (which I use), the OneNote printer doesn't work on 64-bit Windows, and while there is an XPS add-on, the inserted images aren't being OCRed automatically, have to do it manually page by page, which becomes kind of impractical.
Besides, the annotations cannot be indexed or searched easily, right? For example, if one make use of the highlighter, he cannot generate a list of highlighted text, but rather have to go through the entire document to search for them.
And the filesize seems to err on the large end, understandbly, as the content is inserted as images.
Lastly, as you've mentioned, the format is closed.
I can imagine syncing the .one files locally or via the cloud (e.g. Dropbox), the files are self-contained, AFAIK.
Hopefully there will be an (good) Android client besides the iOS and WP ones, soon.
Since I have some books to be scanned manually (probably into TIF/PDF) anyway, OneNote seems to be a good option, as annotating TIF/PDF aren't that easy either.
Cheers.
P.S. Will also be checking out Xournal, suggested in this post
https://www.mobileread.com/forums/sho...54&postcount=2