The PDF annotation features in DTPro2 are robust: circles, rectangles, collapsible sidenotes, post-it style notes, separate annotation pages. (Though all the apparent features don’t seem to be fully implemented yet.) The next steps, I believe, would be to make these added items indexed by content and by item type/characteristics (so that a smartgroup could collect, for example, all the orange sidenotes with a key icon, that contain a particular word, whose host document is in a particular folder) and to implement these annotation features even in RTFD clippings. This last part is key. Though I’m sure implementation is not as simple as it might seem, applying annotation features to RTFDs would effective expand these features to the “whole other half” of DT (one half being PDFs, the other being RTFs, notwithstanding all the file types recognized by DT). I continue to be impressed with the direction they’re taking Dt.
As we’re not using proprietary file formats and don’t want to, that’s at least difficult, maybe impossible. The PDF specification supports annotations, the RTF specification does not.