The beetle is dark because the greyscale values are a bit low. That could be fixed with a gamma filter or the curves tool.
And your logic makes my brain melt. Are you referring to the in-game "natural" color of the creatures? Because I'm talking about color theory. In the screenshots from the survey (and your signature), they are clearly starting with white base sprites and adding a multiplicative color filter. Which I'm sure is how they'd do it in-game with actual pets.
Actually, JC is completely correct on this as far as anyone -- including yourself -- is aware. The 2D client does apply color to grayscale images... when it encounters something that is not a grayscale base, it converts it to grayscale to apply the color to it. Like anything else doing such a conversion, reds will translate different than yellows, et cetera.
I don't believe they've gone in and redone any of the animations or anything for this.
Should they? In an ideal world, yes. UO is not in an ideal state of development 12 years into its life.
If you take a look into INSIDE UO, you can see the various hues that are applied to any particular object. Notice that in MOST cases, they proceed from dark on the left to light on the right. SOME of them proceed differently, and were developed for different creatures and uses (such as fire orange and glacier blue). SOME of them are extremely weird (and were used on gift boxes recently for some strange reason... heh). The hues for the various statues are very interesting, and were made extremely custom to give the statuesque look that they do.
Now, when one of these hues is applied to an object (I'm going to guess that there are particular values of gray they map to) that has grayscale base to it, it applies them to that base. If there is no base, it's obvious it does a conversion and then applies it (otherwise, it wouldn't know where to apply what). The one thing I've NEVER been sure of though is whether the colors map DIRECTLY to an RGB for grayscale in the items that are duo-tone (chairs, dyetubs, et cetera), because those, ONLY the grayscale is affected by hue, anything not grayscale is not hued. It seems to make sense (particulary in 1997) that an if/then would check to see if there was a grayscale range within the object, and either apply totally or just to grayscale. Sadly, every clothing item in the paperdoll since UO:SE has failed to understand WHY the original graphics were done the way they were (grayscale, but yet on shields, borders uncolored), and so they're all colored in the actual graphic file (and sadly, a fairly simple conversion to a limited grayscale palette with particular sections left unchanged if needed) would solve that entire problem of certain clothing looking hideous when hued.
But... long story short, JC is correct about how things are hued. And it's not a small order (on the animation side) to change to something else to my knowledge (though, again, they must already be doing this with hiryus, which suggests it might be possible, though why put that effort into the 2D client at this stage would be a good question).