Many of the same things can happen in sandbox style games. I think there is a tremendous potential for learning in such abstracted environments. What about something like Minecraft, but with abstracted molecules instead of blocks? Problems, like the ones around portraying how molecules inside a cell are constantly jostling against water molecules, could be solved in such environments using design. Many people who play well balanced games at a high level often seem to be learning something about strategy and tactics in particular rule systems. I suspect that there is something educationally valuable in a carefully chosen and implemented rule system.
Also perhaps, it's so much easier to exploit such mechanisms to merely addict people, that overwhelms any value to be gained.