The hyperlink as the base abstraction allowed us to store and navigate individual nodes in a hypertext, but it doesn't work well for collections - thus it provides limited support for programmatic access.
Conversely, pointers & references in programming languages allow for easy handling/transformation of large structures (either loops or recursive traversal), but there have never been a really good visual representation beyond a few nodes, and are difficult to navigate.
A good tool should be based on an abstraction that worked well for linking information at separate places in the data space, and for retrieving collections as a whole. I have my ideas for how that abstraction should work, and even may develop a product around it eventually. ;-)