Blackboard is a terrible LMS, but it is better than the rest of them in terms of its stability, ability to support tens of thousands of students, and integration of grading mechanisms and different containers for content.
Some of the issues you ran into are related to the way the INSTRUCTOR configured the course — there is no reason you cannot have discussions in common boards that everyone could see. Instructors have a great deal of configuration flexibility (although I am with you on the link issues), but have to balance shared information against students cheating or not doing the work. It is much easier to GRADE an isolated environment, even if it is pedagogically inferior.
I agree that there needs to be better tools, but they must take into account the competing goals of encouraging discussion while holding students accountable for doing their work. In a common discussion thread it becomes very easy for one student to hide in the corner, never speaking, and coasting on the coat-tails of the rest of the group. That works fine on Reddit, but horribly in a classroom.
One last comment — people take online classes for flexibility, often because they cannot find a time when everyone can get together — maybe they work evenings, have kids, or have other duties. AMAs and the like generally focus on real-time conversations — the questioner and answerer are both interacting, other people can jump in with comments or related questions, etc. Most online classes cannot do that because it puts a constraint on a class that not all students can meet. Whatever solution emerges, it must be able to handle the asynchronous nature of this beast.