How do you incorporate learning into a game when a game is already about learning?
A game is fun when you can learn directly from the gameplay. It's about learning skills, experimenting, assimilating knowledge through trial and error. It's important to note that learning a skill is a different from learning a fact.
One of the problems with many educational game is that they place knowledge on top of the gameplay--instead of being part of the game, it's tacked on as a sort of afterthought. The wonderful thing about games is that you can experiment in order to learn; you don't need to be lectured.
With this in mind, simply theming a game to a particular topic is not enough to create a learning experience through the game. If you want to have a teaching game about chemistry, for instance, you can't just have a game with a chemistry element. If you want someone to learn from it, it's best to include what you want to learn in the game (e.g. if you want to teach them about changing molecular structure, give them a few molecules and let them manipulate it themselves and see the results of their decision). The knowledge should be something that's discovered through the player's choices or, if you absolutely have to explain a concept, make sure they have to use that knowledge in order to intelligently advance or strategize.
Hopefully this will add some insights, or at least keep these thoughts in light while we're prototyping. These thoughts were collected over the course of a few days, so sorry if they're a bit disjointed, and if anyone has anything to add, it'd benefit!