One of the commentators on my blog (I'm the author of the article), said that ever since TC changed to Facebook comments, he noticed a reduction in critical comments and changed the feel into a "Yes man" type discussions. I guess it depends on how you define quality comments - I prefer people voice their opinions without fear of repercussions. Obviously, this thinking is not appropriate for all cases - if you want product comments for example, by all means Facebook comments might provide the best type.
Fortunately, we haven't gotten any "Yes man" type discussions on our blog yet. Many of our most vocal commenters (who often state contrary opinions to ours) took to the Facebook Comment system well, though we've lost a few too. So far, none of the abusive trolls have come over yet.
Unfortunately, I haven't seen the lively discussions we used to get when using LiveFyre. So there's definitely a trade-off. We're definitely not sold on Facebook Comments yet; it's just our most recent experiment.