At the recent W3Conf Nicolas Gallagher explained that although pseudo-elements have helped us add decorative content to our pages while keeping our HTML clean, this has led to some maintainability issues.
Developer tools can help to some degree, but oftentimes dynamically added content like pseudo-elements or extra elements added via JavaScript are initially harder to track down.
As Nicolas pointed out, the far-future improvement in this area is the Web Components spec, but I think this is something we can improve on right now.