i keep hearing people call for this like its going to happen and be the only way things will be. Look at reddit, look at the history of some of these subs.
there will always be multiple copies of various communities. what software gives us the ability to do is sort and filter and tag (we need to add this) to our hearts content so instance admins and users have control over what comes across thier feeds.
Joined communities will have many of the same centralization problems reddit has now. I've seen this call mostly from users who were on reddit long after it was large. It seems many have no idea that almost every topic on reddit has 4-6 subs around it usually.