The goal of e-learning could not be just economical (saving money on travel or textbooks) or organizational (better and more flexible access to education). E-learning is also about bringing up the pedagogical innovation, introducing the new ways of learning and teaching that meet the needs of knowledge society. Yet there is little empirical proof regarding the strength of this link between new learning environments and innovative educational practices. Teachers seem to use up-to-date Learning Management Systems (LMS) in conservative way, mostly for publishing texts and collecting homework. But maybe we should not blame the teachers, maybe the outdated practices are promoted also by the most modern learning environments? In this paper we are going to argue that trend towards taken-for-granted pedagogical neutrality of LMS is mainly good for marketing purposes. From the viewpoint of pedagogical innovation, the built-in pedagogical neutrality of LMS increases the alienation of theoretical discourse of educational science and technology from the practice of teaching and learning. One solution would be designing a 'pedagogically biased' LMS, as it was done in the Centre for Educational Technology, Tallinn Pedagogical University.