Consider, if you will, car tires. Stop and actually think about them for a little. Somebody figured out that the most effective way to cushion and carry an extremely heavy box of motorized metal was on an extraordinarily thick donut-shaped balloon. Of all the materials such a support could be made out of- such as more obvious things like metal or rock- the most resillient, strong, and generally functional is rubber and air. But mostly air. It's worked so well, nobody's searched for an essentially different answer.
When one thinks about it more, there are many advantages: built-in shock absorption, distortion of tire implies more surface area on ground implies more traction, generally resilient nature of rubber keeps tire from getting bent out of shape with time. It's a good solution- it really is- but what line of thought was it that led the inventor to figure it out? It's easy to see what's right about tires as they exist because they've already been done, but what about before that?
Then there's the entire idea of paved roads: a preference to change the environment to be easier to drive on rather than make machines better at traversing the terrain. It does need to be noted that while it's in one sense safer to drive on easier terrain, it's far more destructive to the environment. It does seem backwards to me: is it really easier to change the environment rather than change the device? I suppose it's rather like heating systems versus sweaters.
A more fundamental counterintuitive thing: parts. Not just the interchangable parts of the Industrial Revolution, but the idea of parts in general: pieces that can be assembled in a variety of ways to make a wide variety of devices. Circuit boards are really simple things, made of just a few fundamental pieces, but they can do very impressive things. There's really nothing intuitive about the production of items completely useless by themselves- at least nails can be useful, but there's not much you can do with just a capacitor.
Just random thoughts, cut short by a *ding* indicating the completion of the cooking of a frozen pizza...