I think that a lot of those issues can be solved. For example, chainbb is a message board interface built on top of steem by @jesta (check out chainbb here). It is possible to get rid of "bot" comment by disqualifying the custom json of it's source.
The goal is this format is for people to be able to host their own forum on their own domain and have full control over it...just like phpbb. I think that might just be what you are looking for.
When it comes to linking in the comment section, I think it is just a matter of relevance. For example, just above, I shared a link that is helpful and add to the discussion. There is no reason for anyone to flag that.
Looking into it. I was not aware that Jesta build a message board, only the stats service. This may and may not work for our purposes. It would depend on the level of control and the potential for censorship (flagging). Can't say much until I really explore what Jesta made so I'll stfu for now.
Finally got my post up, you can check it out here. Tried to not make it a wall of text.
Talk with him on steemit.chat :-) im Ill look into your post