It is because of that why most science games suck:
www.physicsgames.net/ (disclaimer: I love these games and they have merit)

they kill your curiosity by trying to circumvent main stream games ike Call of Duty, Gears of War and Skyrim. Why, you may ask, baffled as I am. Devs try to be good! Forget about that! Now! Discard it!

Have you discarded this foolish idea? Good!

You are ready:

Here is my proposal: Use games like Assassin's Creed, Uncharted even MMOs like SWOTR and amend them with educational content.

Assassin's Creed:
Add action packed missions that end with cool, jaw dropping cut scenes explaining why Byzantine fell to the Ottomans. Create follow up missions where this information needs to be exploited and harnessed. Expound the implications and reward every single step.

Uncharted:
Add action packed missions that reward the player with fractions of a formula that may help elevate a rock to a higher level with less effort by the laws of ballistic flight and reward every single step. Elaborate the problems or add a portal like device that needs exact figures.

Star Wars the old republic
Add a cartographer whose only purpose is to explore planets or caves or anything else by means of Geophysics and Geology. He needs a brute for his missions so he or she hires one that helps keeping cave vermin at bay whilst he or she tries to find new ore. Both receive handsome rewards at the end.

Why trying to invent computer games anew instead of using what is there?

Adhere to the rules of good teaching when adding science content and you are good to go: