I really like to play with mods, especially the tech ones, I enjoy building automated processing systems and factories and bootstrap myself in the style of "The Mysterious Island". Here's a game I really wish would exist (and I think it will, eventually):
Realistic sandbox game based around technology and history of technology. De-emphasize the kinematics, and emphasize other types of physics such as statics, thermodynamics and electromagnetism, and also chemistry, material engineering, biology and geology.
Imagine a game where you could learn about almost any industrial process (including historical ones), ranging from agriculture through chemical engineering to computer-controlled 3D printing.
I wouldn't mind complexity too much. There are people who enjoy flight simulators which are quite complex. It should capture the spirit of common industrial processes, within the first order of approximation.
I think this would be a great game to understand how the modern world is built, on what basis, what it takes for economy to operate. So it would also be very educational in the economics aspect (actually changing focus from money to production would help people to understand economics a lot better).
Current Minecraft is not there though, even with mods. The basic physical laws are not preserved, and often realism is eschewed. It's quite hard to make such a game, because people who know the industrial processes well enough are rare, but I really wish it would exist. And I think it would be highly educational, but mostly in fields of natural sciences and technology.