It is definitely possible to devise a flat UI visual language that would make anything clickable easy to identify, etc.
Two problems: (1) It takes a real and complex design effort, and (2) it's nearly guaranteed to be at odds with the "clean look" aesthetics.
I think it's the minimalist aesthetics that caused the fad of flat design and unidentifiable controls. It strives to make a page / form visually simple, thus hiding its real richness and the irreducible complexity stemming from it. In a misguided attempt to avoid cognitive overload it turns UIs into impenetrable puzzles.
There is a fundamental tension between "clean and simple" and "rich and comfortable". It's much easier to sell "clean and simple" and pretend that it's "intuitive" and does not take any learning. But once you've bought that, and want the power features, they are either not there at all, or are very well hidden ("have you tried triple-drag this to the right?").
Ideally there would be a switch between "beginner mode" and "pro mode", but there's little incentive form the market, because people are just used to put up with the limitations.