I, too, thoroughly enjoy using a tablet. I have been on the hunt for something that has an organizational structure like graphs, paired with support for pen inputs. Right now I've been using OneNote and it is falling victim to the described problem of greater and greater segmentation of ideas.
Right now, it seems like the only real solution is to homebrew something that hits the Microsoft API and associates document IDs to contexts, then launches OneNote for the given document when it comes time to view/edit.
My problem with a graph structure is that ultimately I end up with notes that fit more than one bucket. For that reason I usually gravitate to a structure built on tags.
Right now, it seems like the only real solution is to homebrew something that hits the Microsoft API and associates document IDs to contexts, then launches OneNote for the given document when it comes time to view/edit.