Communities on different instances about the same topic should have the option to essentially federate so a post on one appears on all of them and opening any of them shows you the comments from all of them. This way when lemmy.world is down its not a big deal because posting to any news community federates to all of the communities instead of barely having people see your post. Federation could be decided by the community mods and the comments can have a little “/c/communityname@instance.name” on it so you know which community the comment was originally posted on.
I still don’t get what the point is of multiple instances with the same communities. Your proposal is a fix for a problem that doesnt need to exist IMO. Just have one thematic community be on one specific instance, and a community for a different topic on a different instance
Any instance could go down forever at any point. Should all cat photos ever posted to Lemmy be on one instance? Hell no.
Besides, my idea is about combining any communities into a group. They could be duplicates like you’re assuming, or just closely related, like cat communities. Or I could group together several different sports teams communities into one feed to let me just view those communities when I feel like it.