How is a plain text file more flexible than a PDF? It's trivial programatically to extract plain text from a PDF so it's as least as good as .txt?
Despite that, PDF, especially PDF-A, is the superior format for preserving published content.
Reading plain text files is simpler to do across platforms. If an app on a mobile device just pays attention to the text then that's fine for functionality, I guess. But then I have a problem with the extra formatting being there, unused. Kind of like having a problem with unused CSS in a style sheet just sitting there.