Recently there has been a growing appreciation concerning learner control over the learning/instructional process, leading to the development of mixed-initiative systems where learners are allowed to take varying levels of control. The design of Adaptive Educational Systems (AES) that provide such learner control opportunities through their adaptive and adaptable dimensions, is a challenging research goal that requires a certain understanding of the learning and instructional processes. To this aim, in this chapter we focus on the educational background that should underlie the design of adaptation and learner-system interaction in the context of AES used for Web-based education. We propose an instructional framework that supports a variety of instructional approaches and provides guidelines that unify several processes underlying adaptation such as structuring the domain knowledge, developing the content, and planning individualised support—assessment—learner control opportunities. This framework incorporates a variety of approaches over instruction and assessment, in order to accommodate the diversity of learners’ needs and preferences, and enable them to choose when, what, and how to learn. The theoretical background underlying the design of the framework and the implications for Web-based AES design are also discussed.