I just discovered this site a few weeks ago and I personally like the new format.
My only suggestion is that once I click on full article, I wouln't mind seeing the comments right below the article so I could just continue reading.
The comments link on the home page would have to jump down below the article of course.
This is just an opinion, it's fine the way it is now and may be to much trouble to change. On the other hand, everything related to an article is together.