Interesting. From a quick look, I’m worried how developed Aspen is. Development doesn’t seem to be very active, and it uses Ruby, so I’m not sure how easy it is to integrate. And I’m not sure how it works with multiple files.
A user-defined specification might be very nice, though, especially if people want to add properties to links, or if people consider different things than different note files as nodes, as you mention. Lots of options!