@Jerrico: Rendering an author's reply in a different background color is an excellent idea - noted down :) I thought about that recently, and now that it is mentioned here, it's definitively a great motivation to implement it!
On Wizzley, all comments are in descending order, deliberately, and there is no option to change that, for two reasons:
a) We intent to keep the platform to be consistent. Changing the order of comment on a per-article base is rather confusing for regular readers.
b) With the latest comments on top and only showing the latest 10 comments automatically, Google will regularly find some fresh content on your articles. Otherwise, there will be nothing new in the comments section for Google.
@Sheri: Indenting comments is certainly a great idea and it's been discussed over and over in our team conferences . However, a) it involves a lot of development work, b) not everybody actually likes indented comments, c) it doesn't make things easier for our responsive, mobile layout, as Jerrico pointed out already ...
Personally I think the @username solution works best in all cases and it's quite common practice.
An expert is a man who has made all the mistakes which can be made, in a narrow field.
Niels Bohr (1885-1962)