It's definitely been an issue brought up by our faculty. The 3.1.1 fix for the panels was helpful, but, part of the issue is with the auto-pdf generator. Moodle complements our face-to-face/on-site program, and many of the faculty prefer to do writing annotations on paper. We are a language program so many of the levels only do short amounts (e.g. a paragraph is quite long for some low-levels) and the ability here is simply not as necessary (or as fast) as doing it by hand. I prefer the electronic method either way, but, I'm not teaching the courses so I defer to their preferences. We also have many assignment submissions with Poodll, also making the auto-pdf generator unnecessary. Each time you move through a submission, you have to accept the warning message that a file is corrupt or missing when there simply is no document file in the first place.
As a student who has taken many online courses in Moodle as a graduate student, I completely understand that the majority of asynchronous coursework will be document based, but even when turning in links to something like a Google Doc, or a website, the auto-pdf viewer pane is just completely out of place. The dynamic editing/collaboration ability through Google Docs is far better than just a one way annotation.
I wonder if there would be a way for developers to turn that pain into a web-browser (the way Doctopus and Goobric work) to really put everything in once place if the submission was in fact a link.
It has potential for sure, but there is some design work that needs to be done .