Lots of what I value in a course are conversations and self directed learning on the way to the final assessment. Subjects like history, teacher training, media studies, music - they don't entirely fit into the programmed style of a lesson or scorm module.
So you need functionality to support this alternative kind of approach.
Forums are of course quite good for this, but in Moodle they are still a bit dated: click on reply, and you loose the ability to see any of the other posts, you can't save drafts, add comments, or tags. It is not easy to reference another post (ie there is no permalink link) It is good at last to have student role able to insert pictures, but this core activity is still a many many click process.
Groupwork - Self sign up groups don't exist.
If you run a forum in Moodle set to groups mode you must post individually to each group, you can't post a message to all groups at once - in fact it is difficult to post messages so they can be received by everyone on your course in something like a notice board format or maybe a popup when they next visit. They need to either visit the forum, read a sidebar block or check email.
Quick overviews of student interaction in a forum don't exist.
A tool for a student to manage a personal learning journal/blog doesn't exist at course level. There is no way to set up a personal space per individual short of setting up lots of forums/groupings and groups for every member of a course.
File sharing by student role is not easy.
These are just a few thoughts. I'm sure it could be easier. Even a functional way to do a few of these things would help Moodle be easier to use in more free range learning environments.
I know this goes against the grain of the view of Moodle supporting a 'constructionist' style of course. I'm just saying to be constructive in an LMS could be easier. I find it sad that at the moment we are still sorting out infrastructure (outcomes, assignments) and other aspects (forum development, reporting) are on the back burner.