Many threads on HN and elsewhere get burdened by 1:1 dialog that adds little or no public value. "Why am I being downvoted?" dialogs are one example.
I propose adding a "reply privately" function. A private reply is only visible to commenter and parent, and appears in-thread.
Effectively, this creates a new 1:1 communication channel, without having to add a PM engine, while preserving the message's context.