I think it would be nice to have explicit support to mark groups of duplicates as such... When a certain threshold of users agree that they're indeed duplicates, the two or more submissions could be "glued" together so that they always show up in a tight group on the page.
The different comment threads could be merged in a sensible way, possibly by reallocating threads from comment sections with few comments. Any comment sections that have no more comments or never had any would be disabled. This would avoid having an unnecessarily split discussion of the same topic between multiple comment sections.
