Below are a couple of select quotes from an article discussing electronic medical records written by John Timmer that was published on Ars Technica. The article was not written about AHLTA specifically but the quotes are very applicable:

One of the biggest problems is that the (EMR) systems that are being put in place are largely focused on recreating the current paper-based system in a new medium. In many cases, paper forms are simply being reproduced as an electronic document without any thought given to whether differences in format or function could improve its utility. Worsening the situation, the contents of many of the systems are focused on business outcomes rather than patients. "Care providers spent a great deal of time in electronically documenting what they did for patients," the authors note, "but these providers often said that they were entering the information to comply with regulations or to defend against lawsuits, rather than because they expected someone to use it to improve clinical care."

A key issue is that many EMR systems treat doctors as simple input-output machines—feed them enough data, and they spit out a diagnosis. Instead, the report suggests that doctors build mental models of patients, in much the same way that scientists create models of natural systems. For doctors, the raw data gets combined with subjective impressions, knowledge of past patients, and training, to construct a model that suggests a variety of diagnoses and potential treatments; this guides further tests and treatments to narrow viable options. EMR may speed access to the data but, as currently constructed, doesn't help much with the rest of the process, and the easy access to a lot of extraneous data can actually confuse the model building process.

I believe this insightful commentary describes many of the problems surrounding AHLTA. The strength of AHLTA is that it created a truly worldwide database of electronic medical records. Its weakness is its user interface which provided a simple way of tracking business productivity data but a suboptimal way of storing and retrieving clinical information. There has to be a way to tweak the AHLTA graphical user interface to improve the efficiency of day-to-day clinical medicine practice.