For all the love hypertext receives, I have a great gripe against it: learning through hypertext requires breadth first search over a sea of links.
Documents provide a single-hop link, and it is the reader's job to keep jumping through links until finding all the pieces needed.
DITA is a document format that encourages reuse of document snippets. I think reuse is good in moderation but as much as I'd love each document to be as self-contained as possible, repetition generates extra work for the reader of skipping known pieces (imagine a book where each chapter had 50% repeated paragraphs...). If repetition is involved, it would be nice to track which snippets I've already seen, and possible hide them.
In general, I'd rather authors provided a trail of links (so the extra hops along documents) to cut the search space. It would also be nice to have better "memory" of the places I visited. Currently browsers simply change the color of visited links, but I'd love to know which "trails" that link belonged to, how long ago I visited, etc.
In short, I'd like the experience of navigating hypertext to feel like I have a mentor next to me pointing me to relevant places, encouraging me to not worry about the sea of irrelevant information, etc.