Granted, they may be extremely color-enhanced to bring out details, or perhaps they are false colors, with color added by the software to represent differences in frequency from hues the eye can't see, like infrared. But even so, the colors must reflect differences in chemical composition or physical properties. You would expect everything to be all mixed up into one monochrome pastel soup, but it certainly is not.

I'm just speculating, but I'd guess what we're seeing is a highly stratified atmosphere with different colored compounds predominant at every layer, but strong thermal convective currents are bringing up material from below, and before it has a chance to mix the different gases flow around like multiple paints being mixed. Still, these are gases, not liquids, you would expect them to rapidly mix but they don't. They maintain separation, as if they had different viscosities and temperatures, even surface tensions and densities.

I recall seeing this effect in other images of Jupiter, but I imagined as we zoomed in we would eventually start seeing more mixing and blending at the boundaries. Instead, we see more and more fine structure and detail in the cloud tops the closer we go in. When does it stop?

We really need to send a probe into the atmosphere, taking pictures all the way, until it gets too dark to see anything. Would we eventually see cumulus-like upwellings, stratus-like layers, wisps of cirrus crystals? Right now they just don't look like clouds, although I would guess we're too far out to see them individually, if they're there at all.