I think its a good idea as it would allow the opportunity to respond directly to comments which could in fact be beneficial to the quality of the thread, overall improving the answer.
It's a question of how deep do you nest the comments though? Too deep and it gets hard to follow as the width of the available comment area decreases. How this reflects upon additional code and other formatting would be my concern.
I'd be happy to see either the ability to nest comments one level deep within a parent-comment item or alternatively and possibly an even better solution would be to provide a REPLY TO -> button, much like that found in the chat rooms which means you could in theory then extend a threaded-like reply to system onto the answers as well as the question itself.
Essentially we would leave the current comment format the same, but possibly provide an additional view/toggle which you can switch between to see relationships between comments.
If we thought about there's probably a number of ways we could group related comments together that are not intrusive to the formatting of the site as it currently stands.
How likely are the devs to implement such an idea though?