It makes it harder to make changes. The story you start telling is not what you end up with later, after you've completed all the non-trivial features and major assumptions have fallen through. Going back and fixing the story as you go along is expensive. Writing the story after it's done is too late - the business value is in the product's shipped functionality, not in the development artifacts. We have an alternate…
I'm fairly happy with Leo for "documenting" my Puppet nodes - I create a Leo node for each Puppet node or node regex with a link to the node definition, and a link to the "documentation" node of each class included for that node. Classes have "documentation" nodes which similarly link to their definition, files and templates and to documentation nodes of any classes included by the class. There's no more prose involv…
First of all, there were some encoding conflicts that were introduced when mixing Leo with other editors. When I go back to the project now, it doesn't compile because of the encoding errors. (It's fixable, I'm sure.)
Second, I had more classes than I needed. The secret to writing compact game code is - basically - to write few real classes and rely on plain old data and a large main loop. As it was, they were calling up and down some hierarchy, splitting pieces of the main loop into different classes, running a custom scripting language to drive AI, etc. I had all sorts of ill-considered ideas at the time and no real guidance. It wasn't a _tremendous_ amount of code(running a simple count again, 31,145 LOC with whitespace/comments and 22,372 without), and Leo documented what it all did, but the tool couldn't suggest why it was fundamentally rotten, it just added process on top. By the end I wasn't really using Leo, because it wasn't solving my problems.
Looking back on it now, I have a style that can more naturally accommodate a literary programming approach because I'm more likely to write a straight-line solution first. But I would not rely on an external tool again as I don't want the dependency.