Pedagogy in educational simulations is that layer on top that makes things easier to understand. It includes charts and advice, as well as prereading and after action reviews. Done well, it speeds the learning and avoids the development of superstitious behavior.
One truism of edSims is that the same pedagogy that helps in doing the simulation also helps people understand real life. In fact, some early educational simulations had better pre-canned pedagogy than simulation, and enterprises stripped away the simulation and just deployed the pedagogy.
A nice piece of pedagogy is a constant list of core activities/goals/quests, with updates on little steps either completed or that need to be completed. This is especially useful where there are more than two quests going on at a time, like in this example from Star Wars: Knights of the Old Republic.