One thing to remember is these older consoles don't have the same concept of a "shader" as we do today.
Go back far enough and you'll find the industry trying to settle on quads or triangles for rendering (and we all knew who won)
The games were given basically an immediate mode API into the graphics card and they could do whatever they wanted, whenever they wanted, without warning.
The stutter happened when they were translating the API mentioned above into modern GPU shaders.
When it was on the CPU - They had to determine the effect, generate and compile the modern shaders, and upload that to the GPU, sometimes hundreds of times a second. Then the GPU would take over and display.
Uber shaders took that entire pipeline and moved it into the GPU.
This was low level emulation, just still hitting limits of modern CPUs.
