Content Discontent
One of the more obvious challenges involved in maintaining a deep web presence is simply the fact that the web team holds the technical knowledge, while the content managers hold the domain knowledge. This seems obvious, I know, but it can be a tough hurdle to overcome for a large organization. And there is really no quick fix. Often I hear organizations blaming their CMS or other technology issues for the problems they face with putting content on the web. They think they chose the "wrong" CMS, or they think a redesign will fix the issues they have.
But the technology is not the answer, it usually comes down to the implementation. How are you using the technology? Did you take the needs of the organization into consideration when organizing the workflow? How did you tag your content and build your templates? No external consultant can come in and "fix" the website, no new CMS will be able to shortcut this analysis and work. The internal players need to be bought in and use their domain knowledge to construct the appropriate solution. It all takes time and effort from people who may not have the web as their main focus.
