Why do body plan changes that seem "logical" but don't have, to my layman's perspective, selective advantage, occur? Examples include limb atrophy in aquatic mammals and different shadings of human skin.
Re skin, one could theorize that in the first humans dark skin was selected for due to lower rates of melanoma (don't know if it's true, but it's logical). And I believe scientists will say it's optimum to have light skin, blond hair and blue eyes in northern Europe (let's ignore that the Inuit are not the same color) - but what "forces" that change over generations?
Re whales - are the atrophied legs and pelvis an example of adaptation, or just something that happened randomly? I can see that rear legs might be a hindrance in water, but a hindrance is not the same as a selection characteristic.
A new trait or character of any kind can come in three basic Darwinian "flavors":
adaptive: increases likelihood of successful reproduction in the individual bearing it
maladaptive: decreases likelihood of successful reproduction in the individual bearing it
neutral: does not affect likelihood of successful reproduction in the individual bearing it
Because we are so steeped in Darwinian theory, sometimes we forget about those neutral traits. If a trait doesn't make any difference, but the individual carrying it happens to have a lot of other adaptive traits that make its genes better represented in the next generation, then it's the whole package that can be passed on, including the neutral traits.
I, for one, don't buy the hypothesis that human skin color is necessarily adaptive for reasons of Vitamin D metabolism. As you note, Inuits have darker skin, though one could make the argument that they get their vitamin D from the very fatty mammals they have traditionally hunted. But it still doesn't make a whole lot of sense to me. I think that genetic drift/neutral evolution can play a huge part in making populations what they are.
Let's also not forget about sexual selection, a subset of natural selection. If an individual has a trait that makes him/her sexier to the opposite sex, then that individual will have a reproductive advantage. It was recently discovered that all blue-eyed people on earth are likely descended from a single individual. Either that individual was incredibly lucky, or people of both sexes found blue eyes very attractive, so those blue-eyed individuals got a disproportionate number of mating opportunities.
When it comes to vestigial structures, remember that not only will an ancestral whale with smaller hind limbs (by chance) be better able to move in the water, but also that larger limbs in an aquatic animal can not only be a hindrance, but also are energetically expensive to maintain. Hence, there's a double advantage to those who might have had those smaller limbs: less encumbrance, and more energy for foraging, reproduction, etc. without having to "feed" the larger, useless limbs.
It's all hypothetical, if logical. It's not always possible to reconstruct evolutionary history. But there's a lot more at play than simple adaptiveness.
Hope that helps.