By virtue of their intent and design, course management systems impose limitations on instructional creativity and approach. They aren't designed to encourage innovative teaching. As products marketed to institutions to help them integrate resources, they are designed along the lines of inventory control or commercial enterprise applications.

With the emergence of new learning management systems and virtual learning environments based on alternative pedagogy, and the advent of Web 2.0 applications such as blogs, wikis, and social networking, one thing has become clear: the standardized nature of integrated commercial systems is limiting pedagogy. Although particularly an issue for novice users, it can even pose problems for experienced online instructors.