To use the graph structure fully, you would have to allow each student to progress individually... but then you can't have in the same classroom, listening to the teacher

Well, yes and no. There are methods (usually called within-class groups) that allow students to progress at different paces while being in the same classroom. These methods usually depend a lot on small-group instruction and peer helping. So no, they won't be simply listening to the teacher, at least not all at the same time.