It's the old ideological war between linear° and threaded discussion boards.

And as usual people want the cake and eat it too.

(Threaded discussions with linear order? WTF )

Please note that SO is limiting to 3 "levels" depth. (Question/Answer/Comment- And I am always confused by that structure)

IMHO the only possible answer is a "flexible" adjustment to the needs of the current reader.

I.e. DHTML to optionally show the sub-tree overview like in RAT, reordering the replies, folding and navigating them.

There is for sure no right order for threads, if one reply provokes a large subtree, then the next direct reply is buried behind, even if it's the "second best" reply.

Folding is the only alternative which comes to mind.

BTW: I'm still waiting for an example where another answer was implicitly referenced without linking or naming the author.

I remember rare instances of people talking about "the former reply".

But most replies here are from regulars, which don't do this.

So it's not happening "often"

°) compare phpbb if you don't know what linear boards are, or look at WP https://en.wikipedia.org/wiki/Conversation_threading