I'd say the unintuive part is mostly a problem only if you abuse fragment shaders for something they weren't meant to be used for. All the fancy drawings that people make on shadertoy are cool tricks but you would very rarely do something like that in any practical use case. Fragment shaders weren't meant to be used for making arbitrary drawings that's why you have high level graphic APIs and content creation software.

They were meant to be means for more flexible last stage of more or less traditional GPU pipeline. Normal shader would do something like sample a pixel from texture using UV coordinates already interpolated by GPU (don't even have to convert x,y screen or world coordinates into texture UV yourself), maybe from multiple textures (normal map, bump map, roughness, ...) combine it with light direction and calculate final color for that specific pixel of triangle. But the actual drawing structure comes mostly from geometry and texture not the fragment shader. With popularity of PBR and deferred rendering large fraction of objects can share the same common PBR shader parametrized by textures and only some special effects using custom stuff.

For any programmable system people will explore how far can it be pushed, but it shouldn't be surprise that things get inconvenient and not so intuitive once you go beyond normal use case. I don't think anyone is surprised that computing Fibonacci numbers using C++ templates isn't intuitive.