Alex Cho Snyder in this excellent article describes how he helped design FoldIt a protein folding game.
He mentions the use of Skill Chains from this article. Skill Chains are basically a flowchart of the different skills a player encounters and must master to progress through the game. With respect to educational games, it is a great way to map the educational goals to the gameplay. In the past we’ve generally used tables of skills and how they map into the game. The flow-chart nature of skill chains is superior to tables because the tables imply a linear progression through the skills. Games however are usually not linear and the skill-chains show that.