I have rarely seen meaningful discussion in the comments on articles. Normally I see shallow opinion and by shallow I mean not well supported. People don't typically write half a page worth of response in support of their view in the comment section. The default sorting option is by popularity. Simply put I don't see it as in depth discussion.
I can't speak for the others, but on my part, I've noticed on several occasions a chance for proper discussion, yet I've refrained from even properly starting because the moment you say something enough people might disagree about is the moment you heavily risk getting downvoted - and often if there's substance for a proper discussion, there's also room for disagreement because otherwise there wouldn't necessarily be much to really discuss about. Why would I invest in a proper comment when it has a high risk of getting downvoted to oblivion? That, and articles get buried quickly enough for discussions to get buried as well, and I feel the tree structure of the comment sections also helps bury discussions. For a proper discussion, a traditional forum thread is more suitable due to its greater persistence even without the downvotes, but I can personally say that the downvotes don't help either.
In a way, comment sections feel like Twitter: They're suitable for witty and likeable comments that don't go to any great depth, but they're a poor forum for proper discussions.