E-learning systems have rapidly evolved from generation to another throughout the recent years. Adaptive Educational Hypermedia System (AEHS) provides capabilities to personalize the web-based system according to student's model such as user's interests, needs, preferences, knowledge, and background, which are personal characteristics gathered explicitly or implicitly. The goal of developing AEHS is to achieve an effective and affective learning performance, as well as to get positive impacts on the student through gaining skills and learning experiences. Most AEHS are technologically-driven to transfer knowledge rather than pedagogically-driven focusing on gaining cognitive skills and other experiences. To overcome this gap many researchers considered Cognitive style (CS) as the most important factor for reasoning and predicting individual traits, learning strategies and other preferences. Furthermore many researchers proposed new cognitive factors-rational, intuitive, and interpersonal as the most innate, brain-based, fixed stable preferences to build a robust adaptive student model dynamically and to get positive influence on the affective and effective AEHS. Based on the literature review, we have identified a number of theoretical and technical issues related to the AEHS architecture in relation to the whole brain cognitive style model to achieve an effective learning outcomes .The findings will be used for designing a user model for AEHS.