PDF annotaions is a review tool. They are useless for research notes and organizing them is pain. Also now web pages are a better resource for research or learning in general and bookmarks are incompetent to organize. There is already many applications providing a solution for this issue, albeit not completely. Some too complex, some requires a cloud subscription (though this is a plus for syncronization, even when privacy is disregarded there is the issue of file or database size limits), others do not have certain requirements, rest can only show and annotate only PDF or HTML.
A game project that I had in mind for some time. Even though I had decided to write this game more than six months ago, only previous week I could finally start working on it. It is based on a 2 years old WebGL trial of mine. I have already planned basic gameplay, however overall design is going to be shaped after discussion sessions with the artist (Hasan).