It makes sense that our brains have evolved to be better at calculus than probability. This is a survival trait: calculus is necessary any time you want to kill a rabbit with a sling, but you can get by with only crude estimates of probability (see tiger, run: no need to bother computing the exact probability it will try to eat you :-)
What makes less sense to me is why our brains are so much better at doing math and physics in 2D than 3D.
Sure, 2D is simpler because there are fewer numbers involved, but this is more than just reducing vectors from three to two components. There is something fundamentally mind-warpingly hard about trying to visualize 3D math, where in 2D we would just sketch the problem on the back of an envelope, or construct an imaginary sketch in our mind.
Reality is 3D, or at least does a good job of appearing that way, theoretical physics notwithstanding. So how come my brain can easily remember, compare, and reason about many complex 2D scenarios, yet struggles with even simple 3D? Wouldn't it have been more useful if we had evolved a better ability to process the world the way it truly is?
It seems to me that this quirk of our mental geometry processing explains the everlasting popularity of 2D games. If you stop to think about it, the idea of flattening realistic physics onto a 2D plane is somewhat ridiculous! As babies, we learned the rules of inertia, friction, and gravity, but we have only ever experienced these things in a 3D universe. Yet when we pick up the controls of a 2D platformer, we instantly recognize when physics is working as it should, thinking "yeah, that jump felt nice and realistic", without even noticing an entire axis has been removed!
Brains are weird.