Some great comments make only sense when you read which other (not-so-great) comment it was a sophisticated reply to, so I suggest for the comments that are displayed by default, the comments to which they contain an @reply (if any) should also be displayed.
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Too many scenarios in which the "target statement" of an @reply is not in line with the actual most recent action. I see this has much potential to simply bring out noise, or otherwise simply not have any useful effect. Below are some very common occurrences which this mechanism would fail on.
A comment reply's only importance of activity is to notify the user in question, and because there's a human on the other end of the exchange you can settle for the context clues that a machine cannot detect.