Have you played the Portal games? They include lots of things you mention... they introduce how to use the portal gun, for example, not by explaining stuff but giving you a simplified version first... then the full feature set... and then there are all the other things with different physical properties. I can definitely imagine some Portal Advanced game when you'll actually have to use equations to calculate trajectories.
Nevertheless... I'd really like to be persuaded otherwise, but the ability to read Very Confusing Stuff, without any working model, and make sense of it can't really be avoided after a while. We can't really build a game out of every scientific paper, due to the amount of time required to write a game vs. a page of text... (even though I'd love to play games instead of reading papers. And it sounds definitely doable with CS papers. What about a conference accepting games as submissions?)
I've played the first Portal game for a bit, and I liked it, but haven't finished it because puzzle games aren't that strongly my thing. I wonder whether not liking them much is a benefit or a disadvantage for an edugame designer. :-)
the ability to read Very Confusing Stuff, without any working model, and make sense of it can't really be avoided after a while
True enough. But I don't think that very much of education consists of trying to teach this skill in the first place (though one could certainly argue that it should be taught more), and having a solid background in other stuff should make it easier when you do get to that point.
If it's worth saying, but not worth its own post (even in Discussion), then it goes here.