The disucssion of agile development seems to be anchored in the development of code, from lists of "features," described in Stories, assembled from iterations into a releases. In the domain of "true" complex systems, this approach fails to address the complexity of the system itself.
Here's a clip from a working session I gave on the issue of "Systems Management," or the lack of.
In the absense of the "systems" view, the stories, features, iterations, and releases are driven by the current needs of the user. While this may be appropriate for some problems, there is no taxonomy of what systems it is appropriate for.
This is of special interest for large procurements encountered in Enterprise IT and Federal Government programs.