We had chose to abandon the box style at SitePoint so that the topic lists could be more usable. Unfortunately, because the category badge is used in places other than topic lists the change caused a cascade of other issues that needed to be addressed. None that were impossible to “fix”, but some work was needed.
One of the benefits of the box style is that it has a larger area of background color. Because SitePoint has a black header and a white main, the box style provided for easier distinction where otherwise there would be insufficient contrast. We added a neutral border to help provide better recognition. Another problem was with the hamburger menu. Where prior to the changes in the menu’s display of categories was made “location memory” was possible. After changes were made so that categories changed position “color memory” was possible. Going from box style to bullet style means that more effort is needed to use the hamburger menu to navigate to categories.
I have been living with the change for a while now and I am getting used to it. Though my over all feeling is that UX took a hit for the sake of minimalizing the design of topic lists.
I think that if removing the category column will allow some to have a sidebar, the change will have enough positive and will be worth any negative. And even though a lot can be said for not having a lot of addons (plugins, theme components) it is possible to have the “classic” display.