Yeah but who would use a system like that outside of a small hardcore contingent of techies?
In fact, users could use any service they like.
It would not matter what client you use to reply to me. Your reply would appear on Hacker News, because HN would follow the protocol and accept properly signed comments relayed to it.
In your example HN would still need to retrieve and store billions of messages, handle user authentication, discovery, aggregation, additional data handling (e.g. you want to attach a video, or go live). They will need to monetize _something_. So we are back to square one, just with a much more inconvenient client setup process (like we do right now setting up pop3/smtp/imap).